None
**Instruments Affected**: NIRSpec
Tested on CV3 data
# Create a temporary directory to hold notebook output, and change the working directory to that directory.
from tempfile import TemporaryDirectory
import os
import shutil
data_dir = TemporaryDirectory()
os.chdir(data_dir.name)
# Choose CRDS cache location
use_local_crds_cache = False
crds_cache_tempdir = False
crds_cache_notebook_dir = True
crds_cache_home = False
crds_cache_custom_dir = False
crds_cache_dir_name = ""
if use_local_crds_cache:
if crds_cache_tempdir:
os.environ['CRDS_PATH'] = os.path.join(os.getcwd(), "crds")
elif crds_cache_notebook_dir:
try:
os.environ['CRDS_PATH'] = os.path.join(orig_dir, "crds")
except Exception as e:
os.environ['CRDS_PATH'] = os.path.join(os.getcwd(), "crds")
elif crds_cache_home:
os.environ['CRDS_PATH'] = os.path.join(os.environ['HOME'], 'crds', 'cache')
elif crds_cache_custom_dir:
os.environ['CRDS_PATH'] = crds_cache_dir_name
The library imports relevant to this notebook are aready taken care of by importing the NIRSpec Pipeline Testing Tool.
NOTE: This notebook assumes that the pipeline version to be tested is already installed and its environment is activated.
To be able to run this notebook you need to install NPTT (https://github.com/spacetelescope/nirspec_pipe_testing_tool).
If the installation is successful, you will be able to import NPTT.
import warnings
import psutil
from astropy.io import fits
# Only print a DeprecationWarning the first time it shows up, not every time.
with warnings.catch_warnings():
warnings.simplefilter("once", category=DeprecationWarning)
import jwst
from jwst.pipeline.calwebb_detector1 import Detector1Pipeline
from jwst.assign_wcs.assign_wcs_step import AssignWcsStep
from jwst.msaflagopen.msaflagopen_step import MSAFlagOpenStep
from jwst import datamodels
# The latest version of NPTT is installed in the requirements text file at:
# /jwst_validation_notebooks/environment.yml
# import NPTT
import nirspec_pipe_testing_tool as nptt
# To get data from Artifactory
from ci_watson.artifactory_helpers import get_bigdata
# Make sure that the version used is the right one
pipeline_version = jwst.__version__
nptt_version = nptt.__version__
print("Using jwst pipeline version: ", pipeline_version)
print("Using NPTT version: ", nptt_version)
Using jwst pipeline version: 1.3.1 Using NPTT version: 1.1.19
The test is a comparison of the result of our implementation of the MSA Failed Open Flagging step algorithm versus the pipeline's implementation.
The overlap between the pixels flagged as being affected by failed open shutters are compared in regions large enough in the spectral direction to account for the non-repeatable motion of the grating wheel (a few pixels).
For the test to be considered PASSED, the overlap between the results of the two methods should be greater than or equal to msa_flagging_threshold percent for all failed open shutters affecting more than 100 pixels.
The code for these Multi Object Spectroscopy (MOS) and Integral Field Unit (IFU) tests can be obtained from: https://github.com/spacetelescope/nirspec_pipe_testing_tool/blob/master/nirspec_pipe_testing_tool/calwebb_spec2_pytests/auxiliary_code/msa_flagging_testing.py. This pipeline step and the associated pytests are skipped if data is Fixed Slits (FS) or Bright Object Time Series (BOTS).
The input file is defined in the variable input_file (see section Testing Data Set and Variable Setup).
Step description: https://jwst-pipeline.readthedocs.io/en/latest/jwst/msaflagopen/index.html
Pipeline code: https://github.com/spacetelescope/jwst/tree/master/jwst/msaflagopen
If the test PASSED this means that all slitlets or slices individually passed the test. However, if ony one individual slitlet (for MOS data) or slice (for IFU data) test failed, the whole test will be reported as FAILED.
A short description and link to the page: https://outerspace.stsci.edu/display/JWSTCC/Vanilla+MSA+Failed+Open+Flagging
Acronymns used in this notebook:
pipeline: calibration pipeline
cal_detector1: calibration pipeline Stage 1, detector processing
spec2: calibration pipeline spectroscopic Stage 2, spectroscopic processing
NPTT: NIRSpec Pipeline Testing Tool
The pipeline can be run from the command line in two variants: full or per step.
To run the spec2 pipeline in full use the command:
$ strun jwst.pipeline.Spec2Pipeline jwtest_rate.fits
where jwtest_rate.fits is the output of cal_detector1.
To only run the msa_flagging step, use the command:
$ strun jwst.msaflagopen.msaflagopen_step jwtest_assign_wcs.fits
where jwtest_assign_wcs.fits is the output of the previous step, assign_wcs.
NIRSpec TA data will be run through the calwebb_detector1 and the imaging2 pipelines. The imaging pipeline can be run with the following command:
$ strun jwst.pipeline.Image2Pipeline jwtest_rate.fits
These options are also callable from a script with the testing environment active. The Python call for running the pipeline in full or by step are:
$\gt$ from jwst.pipeline.calwebb_spec2 import Spec2Pipeline
$\gt$ Spec2Pipeline.call(jwtest_rate.fits)
or
$\gt$ from jwst.msaflagopen.msaflagopen_step import msaflagopen_step
$\gt$ msaflagopen_step.call(jwtest_rate.fits)
For the imaging pipeline the call would be as follows:
$\gt$ from jwst.pipeline.calwebb_image2 import Image2Pipeline
$\gt$ Image2Pipeline.call(jwtest_rate.fits)
NPTT can run the spec2 pipeline either in full or per step, as well as the imaging pipeline in full. In this notebook we will use NPTT to run the pipeline and the validation tests. To run NPTT, follow the directions in the corresponding repo page.
All testing data is from the CV3 campaign. We chose these files because this is our most complete data set, i.e. all modes and filter-grating combinations.
Data used for testing:
testing_data = {
'mos_prism_clear':{
'uncal_file_nrs1': 'mos_prism_nrs1_uncal.fits',
'uncal_file_nrs2': 'mos_prism_nrs2_uncal.fits',
'msa_shutter_config': 'V0030006000104_msa.fits' },
'mos_g140m_f100lp':{
'uncal_file_nrs1': 'mos_g140m_line1_NRS1_uncal.fits',
'uncal_file_nrs2': 'mos_g140m_line1_NRS2_uncal.fits',
'msa_shutter_config': 'V8460001000101_msa.fits' },
'ifu_prism_clear':{
'uncal_file_nrs1': 'ifu_prism_nrs1_uncal.fits',
'uncal_file_nrs2': 'ifu_prism_nrs2_uncal.fits',
'msa_shutter_config': None },
'ifu_g395h_f290lp':{
'uncal_file_nrs1': 'ifu_g395h_f290lp_nrs1_uncal.fits',
'uncal_file_nrs2': 'ifu_g395h_f290lp_nrs2_uncal.fits',
'msa_shutter_config': None }
}
# define function to pull data from Artifactory
def get_artifactory_file(data_set_dict, detector):
"""This function creates a list with all the files needed per detector to run the test.
Args:
data_set_dict: dictionary, contains inputs for a specific mode and configuration
detector: string, either nrs1 or nrs2
Returns:
data: list, contains all files needed to run test
"""
files2obtain = ['uncal_file_nrs1', 'msa_shutter_config']
data = []
for file in files2obtain:
data_file = None
try:
if '_nrs' in file and '2' in detector:
file = file.replace('_nrs1', '_nrs2')
data_file = get_bigdata('jwst_validation_notebooks',
'validation_data',
'nirspec_data',
data_set_dict[file])
except TypeError:
data.append(None)
continue
data.append(data_file)
return data
# Set common NPTT switches for this test
# accepted threshold difference with respect to benchmark files
msa_flagging_threshold = 99.5
# other NPTT variables
stellarity = None
operability_ref = None
source_type = None
save_figs = False
show_figs = True
debug = False
verbose = False
# Get the data
results_dict = {}
detectors = ['nrs1', 'nrs2']
for mode_config, data_set_dict in testing_data.items():
for det in detectors:
print('Testing files for detector: ', det)
data = get_artifactory_file(data_set_dict, det)
uncal_file, msa_shutter_config = data
print('Working with uncal_file: ', uncal_file)
uncal_basename = os.path.basename(uncal_file)
# Run the stage 1 pipeline
rate_object = Detector1Pipeline.call(uncal_file)
# Make sure the MSA shutter configuration file is set up correctly
if msa_shutter_config is not None:
msa_metadata = rate_object.meta.instrument.msa_metadata_file
print(msa_metadata)
if msa_metadata is None or msa_metadata == 'N/A':
rate_object.meta.instrument.msa_metadata_file = msa_shutter_config
# Run the stage 2 pipeline steps
try:
pipe_object = AssignWcsStep.call(rate_object)
skip_file = False
except:
print("An error occured with AssignWcs. Likely: No open slits fall on detector", det)
print("Skipping test for this file. \n")
skip_file = True
if not skip_file:
msa_flagging_object = MSAFlagOpenStep.call(pipe_object)
# Run the validation test
%matplotlib inline
result, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.msa_flagging_testing.run_msa_flagging_testing(
msa_flagging_object,
msa_flagging_threshold = msa_flagging_threshold,
rate_obj = rate_object,
stellarity = stellarity,
operability_ref = operability_ref,
save_figs = save_figs,
show_figs = show_figs,
source_type = source_type,
debug = debug)
else:
result = 'skipped'
# Did the test pass
print("Did msa_flagging validation test pass? ", result, "\n\n")
rd = {uncal_basename: result}
results_dict.update(rd)
# close all open files
psutil.Process().open_files()
closing_files = []
for fd in psutil.Process().open_files():
if data_dir.name in fd.path:
closing_files.append(fd)
for fd in closing_files:
try:
if verbose:
print('Closing file: ', fd)
open(fd.fd).close()
except:
if verbose:
print('File already closed: ', fd)
Testing files for detector: nrs1 Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/mos_prism_nrs1_uncal.fits
2021-10-05 12:24:34,108 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-10-05 12:24:34,138 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-10-05 12:24:34,140 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-10-05 12:24:34,142 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-10-05 12:24:34,145 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-10-05 12:24:34,147 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-10-05 12:24:34,149 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-10-05 12:24:34,150 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-10-05 12:24:34,152 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-10-05 12:24:34,154 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-10-05 12:24:34,155 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-10-05 12:24:34,157 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-10-05 12:24:34,159 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-10-05 12:24:34,160 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-10-05 12:24:34,163 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-10-05 12:24:34,165 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-10-05 12:24:34,167 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-10-05 12:24:34,169 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2021-10-05 12:24:34,369 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/mos_prism_nrs1_uncal.fits',).
2021-10-05 12:24:34,379 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-10-05 12:24:34,543 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'mos_prism_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-10-05 12:24:34,554 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0086.fits'.
2021-10-05 12:24:34,556 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits'.
2021-10-05 12:24:34,559 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits'.
2021-10-05 12:24:34,561 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits'.
2021-10-05 12:24:34,563 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-10-05 12:24:34,564 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits'.
2021-10-05 12:24:34,565 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_refpix_0022.fits'.
2021-10-05 12:24:34,568 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-10-05 12:24:34,569 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-10-05 12:24:34,570 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits'.
2021-10-05 12:24:34,572 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0113.fits'.
2021-10-05 12:24:34,574 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-10-05 12:24:34,575 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-10-05 12:24:34,575 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-10-05 12:24:35,073 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-10-05 12:24:35,076 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:24:35,301 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-10-05 12:24:35,303 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-10-05 12:24:35,305 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-10-05 12:24:35,442 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-10-05 12:24:35,445 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:24:35,466 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits
2021-10-05 12:24:35,942 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-10-05 12:24:36,115 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-10-05 12:24:36,117 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:24:36,138 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits
2021-10-05 12:24:36,991 - stpipe.Detector1Pipeline.saturation - INFO - Detected 9869 saturated pixels
2021-10-05 12:24:37,039 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-10-05 12:24:37,076 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-10-05 12:24:37,245 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-10-05 12:24:37,247 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:24:37,248 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-10-05 12:24:37,250 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-10-05 12:24:37,394 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-10-05 12:24:37,396 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:24:37,417 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0113.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stdatamodels/validate.py:34: ValidationWarning: While validating meta.exposure.readpatt the following error occurred:
'ALLIRS2' is not one of ['ACQ1', 'ACQ2', 'BRIGHT1', 'BRIGHT2', 'DEEP2', 'DEEP8', 'FAST', 'FASTGRPAVG', 'FASTGRPAVG8', 'FASTGRPAVG16', 'FASTGRPAVG32', 'FASTGRPAVG64', 'FASTR1', 'FASTR100', 'FGS', 'FGS60', 'FGS8370', 'FGS840', 'FGSRAPID', 'FINEGUIDE', 'ID', 'MEDIUM2', 'MEDIUM8', 'NIS', 'NISRAPID', 'NRS', 'NRSIRS2', 'NRSN16R4', 'NRSN32R8', 'NRSN8R2', 'NRSRAPID', 'NRSIRS2RAPID', 'NRSRAPIDD1', 'NRSRAPIDD2', 'NRSRAPIDD6', 'NRSSLOW', 'RAPID', 'SHALLOW2', 'SHALLOW4', 'SLOW', 'SLOWR1', 'TRACK', 'ANY', 'N/A']
Failed validating 'enum' in schema:
OrderedDict([('title', 'Readout pattern'),
('type', 'string'),
('enum',
['ACQ1',
'ACQ2',
'BRIGHT1',
'BRIGHT2',
'DEEP2',
'DEEP8',
'FAST',
'FASTGRPAVG',
'FASTGRPAVG8',
'FASTGRPAVG16',
'FASTGRPAVG32',
'FASTGRPAVG64',
'FASTR1',
'FASTR100',
'FGS',
'FGS60',
'FGS8370',
'FGS840',
'FGSRAPID',
'FINEGUIDE',
'ID',
'MEDIUM2',
'MEDIUM8',
'NIS',
'NISRAPID',
'NRS',
'NRSIRS2',
'NRSN16R4',
'NRSN32R8',
'NRSN8R2',
'NRSRAPID',
'NRSIRS2RAPID',
'NRSRAPIDD1',
'NRSRAPIDD2',
'NRSRAPIDD6',
'NRSSLOW',
'RAPID',
'SHALLOW2',
'SHALLOW4',
'SLOW',
'SLOWR1',
'TRACK',
'ANY',
'N/A']),
('fits_ke ...
warnings.warn(errmsg, ValidationWarning)
2021-10-05 12:24:37,947 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-10-05 12:24:38,154 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-10-05 12:24:38,156 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-10-05 12:24:38,176 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /grp/crds/cache/references/jwst/jwst_nirspec_refpix_0022.fits
2021-10-05 12:24:52,195 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-10-05 12:24:52,617 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-10-05 12:24:52,619 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:24:52,640 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits
2021-10-05 12:24:53,584 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-10-05 12:24:53,774 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-10-05 12:24:53,776 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'dark_output': None}
2021-10-05 12:24:53,875 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0086.fits
2021-10-05 12:24:58,315 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=4, nframes=1, groupgap=0
2021-10-05 12:24:58,320 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=65, nframes=1, groupgap=0
2021-10-05 12:24:59,042 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-10-05 12:24:59,716 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-10-05 12:24:59,718 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}
2021-10-05 12:24:59,769 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-10-05 12:24:59,885 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2021-10-05 12:24:59,967 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2021-10-05 12:25:00,014 - stpipe.Detector1Pipeline.jump - INFO - Using 1 core for jump detection
2021-10-05 12:25:00,280 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-10-05 12:25:00,436 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-10-05 12:25:02,255 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 0 pixels with at least one CR and at least four groups
2021-10-05 12:25:02,256 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 19712 pixels with at least one CR and three groups
2021-10-05 12:25:02,257 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 8617 pixels with at least one CR and two groups
2021-10-05 12:25:03,016 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 2.73415 sec
2021-10-05 12:25:03,018 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 3.248787
2021-10-05 12:25:03,021 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-10-05 12:25:03,134 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-10-05 12:25:03,135 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-10-05 12:25:03,208 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2021-10-05 12:25:03,254 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2021-10-05 12:25:03,299 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-10-05 12:25:03,300 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/jwst/ramp_fitting/ols_fit.py:1169: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int, :, :, :] *= (segs_4[num_int, :, :, :] > 0)
2021-10-05 12:25:17,641 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 4
2021-10-05 12:25:17,642 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-10-05 12:25:17,871 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-10-05 12:25:18,027 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-10-05 12:25:18,029 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:25:18,090 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-10-05 12:25:18,091 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-10-05 12:25:18,094 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:25:18,194 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-10-05 12:25:18,196 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:25:18,258 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-10-05 12:25:18,259 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-10-05 12:25:18,262 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:25:18,263 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-10-05 12:25:18,265 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-10-05 12:25:18,274 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:25:18,435 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-10-05 12:25:18,437 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
N/A
2021-10-05 12:25:18,592 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2021-10-05 12:25:18,629 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2021-10-05 12:25:18,630 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2021-10-05 12:25:18,631 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2021-10-05 12:25:18,632 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:25:18,891 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS1: [3, 4]
2021-10-05 12:25:18,891 - stpipe.AssignWcsStep - INFO - Computing WCS for 2 open slitlets
2021-10-05 12:25:18,919 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2021-10-05 12:25:18,920 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2021-10-05 12:25:18,920 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2021-10-05 12:25:18,921 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:25:18,930 - stpipe.AssignWcsStep - INFO - SPORDER= 0, wrange=[6e-07, 5.3e-06]
2021-10-05 12:25:19,053 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 1
2021-10-05 12:25:19,054 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 2
2021-10-05 12:25:19,055 - stpipe.AssignWcsStep - INFO - There are 1 open slits in quadrant 3
2021-10-05 12:25:19,066 - stpipe.AssignWcsStep - INFO - There are 1 open slits in quadrant 4
2021-10-05 12:25:19,079 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 5
2021-10-05 12:25:19,209 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0034.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0028.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/V0030006000104_msa.fits'}
2021-10-05 12:25:19,360 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-10-05 12:25:19,367 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-10-05 12:25:19,377 - stpipe.MSAFlagOpenStep - INFO - MSAFlagOpenStep instance created.
2021-10-05 12:25:19,498 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep running with args (<ImageModel(2048, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-10-05 12:25:19,500 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-10-05 12:25:19,517 - stpipe.MSAFlagOpenStep - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2021-10-05 12:25:19,519 - stpipe.JwstStep - INFO - JwstStep instance created.
2021-10-05 12:25:19,647 - stpipe.MSAFlagOpenStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2021-10-05 12:25:19,648 - stpipe.MSAFlagOpenStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2021-10-05 12:25:19,649 - stpipe.MSAFlagOpenStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2021-10-05 12:25:19,650 - stpipe.MSAFlagOpenStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:25:19,660 - stpipe.MSAFlagOpenStep - INFO - SPORDER= 0, wrange=[6e-07, 5.3e-06]
2021-10-05 12:25:19,782 - stpipe.MSAFlagOpenStep - INFO - There are 5 open slits in quadrant 1
2021-10-05 12:25:19,827 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 2
2021-10-05 12:25:19,856 - stpipe.MSAFlagOpenStep - INFO - There are 9 open slits in quadrant 3
2021-10-05 12:25:19,932 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 4
2021-10-05 12:25:19,959 - stpipe.MSAFlagOpenStep - INFO - There are 0 open slits in quadrant 5
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-10-05 12:25:31,410 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep done
2021-10-05 12:25:32,369 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:25:32,379 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:25:32,617 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-10-05 12:25:32,619 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.45, 'slit_y_high': 0.45}
2021-10-05 12:25:32,760 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2021-10-05 12:25:32,811 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2021-10-05 12:25:32,812 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2021-10-05 12:25:32,813 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2021-10-05 12:25:32,814 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:25:32,999 - stpipe.AssignWcsStep - INFO - Removing slit 1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:25:33,039 - stpipe.AssignWcsStep - INFO - Removing slit 2 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:25:33,196 - stpipe.AssignWcsStep - INFO - Removing slit 6 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:25:33,235 - stpipe.AssignWcsStep - INFO - Removing slit 7 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:25:33,275 - stpipe.AssignWcsStep - INFO - Removing slit 8 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:25:33,706 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS1: [3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
2021-10-05 12:25:33,707 - stpipe.AssignWcsStep - INFO - Computing WCS for 14 open slitlets
2021-10-05 12:25:33,739 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2021-10-05 12:25:33,739 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2021-10-05 12:25:33,740 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2021-10-05 12:25:33,741 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:25:33,750 - stpipe.AssignWcsStep - INFO - SPORDER= 0, wrange=[6e-07, 5.3e-06]
2021-10-05 12:25:33,878 - stpipe.AssignWcsStep - INFO - There are 3 open slits in quadrant 1
2021-10-05 12:25:33,912 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 2
2021-10-05 12:25:33,913 - stpipe.AssignWcsStep - INFO - There are 9 open slits in quadrant 3
2021-10-05 12:25:33,993 - stpipe.AssignWcsStep - INFO - There are 2 open slits in quadrant 4
2021-10-05 12:25:34,012 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 5
2021-10-05 12:25:34,435 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0034.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0028.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': 'fopens_metafile_msa.fits'}
2021-10-05 12:25:34,788 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-10-05 12:25:34,795 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
Working with slit/slice: 3 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[2007 2048] [1629 1641]] Max value in slity array (ignoring NANs): 0.49934753059464704 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 4 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[2017 2048] [1319 1331]] Max value in slity array (ignoring NANs): 0.4992600265017523 percentage of F/O trace that was flagged: 96.6
Working with slit/slice: 5 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[1873 2048] [1590 1601]] Max value in slity array (ignoring NANs): 0.49970473402574966 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 9 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[1511 1939] [1261 1271]] Max value in slity array (ignoring NANs): 0.47541638939121267 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 10 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[1515 1943] [1230 1241]] Max value in slity array (ignoring NANs): 0.4999677623917731 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 11 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[1160 1594] [1827 1837]] Max value in slity array (ignoring NANs): 0.4975789418957247 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 12 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[1213 1643] [1251 1261]] Max value in slity array (ignoring NANs): 0.4911821622434934 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 13 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 920 1356] [1692 1703]] Max value in slity array (ignoring NANs): 0.4997273932113973 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 14 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 819 1255] [1632 1643]] Max value in slity array (ignoring NANs): 0.4998008389664905 percentage of F/O trace that was flagged: 99.8
Working with slit/slice: 15 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 736 1172] [1376 1388]] Max value in slity array (ignoring NANs): 0.49973439389336194 percentage of F/O trace that was flagged: 99.8
Working with slit/slice: 16 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 656 1096] [1862 1874]] Max value in slity array (ignoring NANs): 0.49919217087642653 percentage of F/O trace that was flagged: 99.8
Working with slit/slice: 17 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 707 1144] [1517 1528]] Max value in slity array (ignoring NANs): 0.49950881420114257 percentage of F/O trace that was flagged: 99.8
Working with slit/slice: 18 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 859 1287] [ 205 215]] Max value in slity array (ignoring NANs): 0.4985413500738489 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 19 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 761 1193] [ 623 634]] Max value in slity array (ignoring NANs): 0.4996526774597415 percentage of F/O trace that was flagged: 99.8
* One or more traces show msa_flagging match < 99.5
See results above per trace.
*** Final result for msa_flagging test will be reported as FAILED ***
('* MSA flagging validation test took ', '17.495537519454956 seconds to finish.')
Did msa_flagging validation test pass? False
Testing files for detector: nrs2
Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/mos_prism_nrs2_uncal.fits
2021-10-05 12:25:49,793 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-10-05 12:25:49,810 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-10-05 12:25:49,812 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-10-05 12:25:49,813 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-10-05 12:25:49,815 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-10-05 12:25:49,816 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-10-05 12:25:49,818 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-10-05 12:25:49,821 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-10-05 12:25:49,823 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-10-05 12:25:49,826 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-10-05 12:25:49,832 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-10-05 12:25:49,834 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-10-05 12:25:49,836 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-10-05 12:25:49,838 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-10-05 12:25:49,840 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-10-05 12:25:49,842 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-10-05 12:25:49,844 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-10-05 12:25:49,845 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/mos_prism_nrs2_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-10-05 12:25:50,186 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/mos_prism_nrs2_uncal.fits',).
2021-10-05 12:25:50,196 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-10-05 12:25:50,374 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'mos_prism_nrs2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-10-05 12:25:50,385 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0087.fits'.
2021-10-05 12:25:50,387 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits'.
2021-10-05 12:25:50,389 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0021.fits'.
2021-10-05 12:25:50,391 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0011.fits'.
2021-10-05 12:25:50,392 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-10-05 12:25:50,393 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits'.
2021-10-05 12:25:50,395 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_refpix_0020.fits'.
2021-10-05 12:25:50,397 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-10-05 12:25:50,397 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-10-05 12:25:50,398 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0021.fits'.
2021-10-05 12:25:50,400 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0114.fits'.
2021-10-05 12:25:50,402 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-10-05 12:25:50,402 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-10-05 12:25:50,403 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-10-05 12:25:50,886 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-10-05 12:25:50,889 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:25:51,131 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-10-05 12:25:51,133 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-10-05 12:25:51,137 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-10-05 12:25:51,330 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-10-05 12:25:51,331 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:25:51,352 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0011.fits
2021-10-05 12:25:51,787 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-10-05 12:25:51,921 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-10-05 12:25:51,923 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:25:51,943 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0021.fits
2021-10-05 12:25:52,674 - stpipe.Detector1Pipeline.saturation - INFO - Detected 5379 saturated pixels
2021-10-05 12:25:52,704 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-10-05 12:25:52,733 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-10-05 12:25:52,887 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-10-05 12:25:52,889 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:25:52,890 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-10-05 12:25:52,892 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-10-05 12:25:53,014 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-10-05 12:25:53,016 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:25:53,036 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0114.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stdatamodels/validate.py:34: ValidationWarning: While validating meta.exposure.readpatt the following error occurred:
'ALLIRS2' is not one of ['ACQ1', 'ACQ2', 'BRIGHT1', 'BRIGHT2', 'DEEP2', 'DEEP8', 'FAST', 'FASTGRPAVG', 'FASTGRPAVG8', 'FASTGRPAVG16', 'FASTGRPAVG32', 'FASTGRPAVG64', 'FASTR1', 'FASTR100', 'FGS', 'FGS60', 'FGS8370', 'FGS840', 'FGSRAPID', 'FINEGUIDE', 'ID', 'MEDIUM2', 'MEDIUM8', 'NIS', 'NISRAPID', 'NRS', 'NRSIRS2', 'NRSN16R4', 'NRSN32R8', 'NRSN8R2', 'NRSRAPID', 'NRSIRS2RAPID', 'NRSRAPIDD1', 'NRSRAPIDD2', 'NRSRAPIDD6', 'NRSSLOW', 'RAPID', 'SHALLOW2', 'SHALLOW4', 'SLOW', 'SLOWR1', 'TRACK', 'ANY', 'N/A']
Failed validating 'enum' in schema:
OrderedDict([('title', 'Readout pattern'),
('type', 'string'),
('enum',
['ACQ1',
'ACQ2',
'BRIGHT1',
'BRIGHT2',
'DEEP2',
'DEEP8',
'FAST',
'FASTGRPAVG',
'FASTGRPAVG8',
'FASTGRPAVG16',
'FASTGRPAVG32',
'FASTGRPAVG64',
'FASTR1',
'FASTR100',
'FGS',
'FGS60',
'FGS8370',
'FGS840',
'FGSRAPID',
'FINEGUIDE',
'ID',
'MEDIUM2',
'MEDIUM8',
'NIS',
'NISRAPID',
'NRS',
'NRSIRS2',
'NRSN16R4',
'NRSN32R8',
'NRSN8R2',
'NRSRAPID',
'NRSIRS2RAPID',
'NRSRAPIDD1',
'NRSRAPIDD2',
'NRSRAPIDD6',
'NRSSLOW',
'RAPID',
'SHALLOW2',
'SHALLOW4',
'SLOW',
'SLOWR1',
'TRACK',
'ANY',
'N/A']),
('fits_ke ...
warnings.warn(errmsg, ValidationWarning)
2021-10-05 12:25:53,508 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-10-05 12:25:53,637 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-10-05 12:25:53,639 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-10-05 12:25:53,658 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /grp/crds/cache/references/jwst/jwst_nirspec_refpix_0020.fits
2021-10-05 12:26:07,847 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-10-05 12:26:08,127 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-10-05 12:26:08,130 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:26:08,152 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0021.fits
2021-10-05 12:26:08,936 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-10-05 12:26:09,105 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-10-05 12:26:09,107 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'dark_output': None}
2021-10-05 12:26:09,181 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0087.fits
2021-10-05 12:26:13,586 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=4, nframes=1, groupgap=0
2021-10-05 12:26:13,587 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=65, nframes=1, groupgap=0
2021-10-05 12:26:14,181 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-10-05 12:26:14,804 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-10-05 12:26:14,806 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}
2021-10-05 12:26:14,842 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-10-05 12:26:14,892 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits
2021-10-05 12:26:15,001 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits
2021-10-05 12:26:15,054 - stpipe.Detector1Pipeline.jump - INFO - Using 1 core for jump detection
2021-10-05 12:26:15,328 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-10-05 12:26:15,483 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-10-05 12:26:17,285 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 0 pixels with at least one CR and at least four groups
2021-10-05 12:26:17,286 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 7787 pixels with at least one CR and three groups
2021-10-05 12:26:17,287 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 3636 pixels with at least one CR and two groups
2021-10-05 12:26:17,667 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 2.33709 sec
2021-10-05 12:26:17,670 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 2.827139
2021-10-05 12:26:17,673 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-10-05 12:26:17,812 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-10-05 12:26:17,814 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-10-05 12:26:17,889 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits
2021-10-05 12:26:17,933 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits
2021-10-05 12:26:17,981 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-10-05 12:26:17,982 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/jwst/ramp_fitting/ols_fit.py:1169: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int, :, :, :] *= (segs_4[num_int, :, :, :] > 0)
2021-10-05 12:26:31,879 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 4
2021-10-05 12:26:31,880 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-10-05 12:26:32,108 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-10-05 12:26:32,276 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-10-05 12:26:32,278 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:26:32,340 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-10-05 12:26:32,341 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-10-05 12:26:32,343 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:26:32,455 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-10-05 12:26:32,457 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:26:32,519 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-10-05 12:26:32,520 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-10-05 12:26:32,522 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:26:32,524 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-10-05 12:26:32,525 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-10-05 12:26:32,534 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:26:32,652 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-10-05 12:26:32,654 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
N/A
2021-10-05 12:26:32,791 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1 2021-10-05 12:26:32,824 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg 2021-10-05 12:26:32,825 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg 2021-10-05 12:26:32,826 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg 2021-10-05 12:26:32,827 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg 2021-10-05 12:26:33,002 - stpipe.AssignWcsStep - INFO - Removing slit 3 from the list of open slits because the WCS bounding_box is completely outside the detector. 2021-10-05 12:26:33,041 - stpipe.AssignWcsStep - INFO - Removing slit 4 from the list of open slits because the WCS bounding_box is completely outside the detector. 2021-10-05 12:26:33,042 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS2: [] 2021-10-05 12:26:33,042 - stpipe.AssignWcsStep - CRITICAL - No open slits fall on detector NRS2.
An error occured with AssignWcs. Likely: No open slits fall on detector nrs2 Skipping test for this file. Did msa_flagging validation test pass? skipped Testing files for detector: nrs1 Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/mos_g140m_line1_NRS1_uncal.fits
2021-10-05 12:26:33,884 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-10-05 12:26:33,899 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-10-05 12:26:33,901 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-10-05 12:26:33,903 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-10-05 12:26:33,904 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-10-05 12:26:33,906 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-10-05 12:26:33,908 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-10-05 12:26:33,909 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-10-05 12:26:33,911 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-10-05 12:26:33,912 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-10-05 12:26:33,914 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-10-05 12:26:33,915 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-10-05 12:26:33,916 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-10-05 12:26:33,918 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-10-05 12:26:33,919 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-10-05 12:26:33,921 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-10-05 12:26:33,923 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-10-05 12:26:33,924 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/mos_g140m_line1_NRS1_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-10-05 12:26:34,124 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/mos_g140m_line1_NRS1_uncal.fits',).
2021-10-05 12:26:34,134 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-10-05 12:26:34,262 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'mos_g140m_line1_NRS1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-10-05 12:26:34,274 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0140.fits'.
2021-10-05 12:26:34,276 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits'.
2021-10-05 12:26:34,278 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0019.fits'.
2021-10-05 12:26:34,280 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0024.fits'.
2021-10-05 12:26:34,282 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-10-05 12:26:34,283 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits'.
2021-10-05 12:26:34,285 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2021-10-05 12:26:34,286 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-10-05 12:26:34,286 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-10-05 12:26:34,287 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0023.fits'.
2021-10-05 12:26:34,289 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0087.fits'.
2021-10-05 12:26:34,291 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-10-05 12:26:34,292 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-10-05 12:26:34,293 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-10-05 12:26:34,822 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-10-05 12:26:34,825 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:26:34,994 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-10-05 12:26:34,995 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-10-05 12:26:34,997 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-10-05 12:26:35,189 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-10-05 12:26:35,191 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:26:35,211 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0024.fits
2021-10-05 12:26:35,675 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-10-05 12:26:35,868 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-10-05 12:26:35,870 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:26:35,890 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0023.fits
2021-10-05 12:26:36,356 - stpipe.Detector1Pipeline.saturation - INFO - Detected 58922 saturated pixels
2021-10-05 12:26:36,390 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-10-05 12:26:36,400 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-10-05 12:26:36,594 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-10-05 12:26:36,597 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:26:36,598 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-10-05 12:26:36,599 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-10-05 12:26:36,781 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-10-05 12:26:36,783 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:26:36,807 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0087.fits
2021-10-05 12:26:37,100 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-10-05 12:26:37,287 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-10-05 12:26:37,289 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-10-05 12:26:37,299 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2021-10-05 12:26:37,300 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2021-10-05 12:26:37,300 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2021-10-05 12:26:37,301 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.000000
2021-10-05 12:26:37,302 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = True
2021-10-05 12:26:39,758 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-10-05 12:26:39,952 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-10-05 12:26:39,954 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:26:39,976 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0019.fits
2021-10-05 12:26:40,824 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-10-05 12:26:40,988 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-10-05 12:26:40,990 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'dark_output': None}
2021-10-05 12:26:41,009 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0140.fits
2021-10-05 12:26:41,289 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=6, nframes=1, groupgap=0
2021-10-05 12:26:41,291 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=10, nframes=1, groupgap=0
2021-10-05 12:26:41,554 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-10-05 12:26:41,731 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-10-05 12:26:41,734 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}
2021-10-05 12:26:41,743 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-10-05 12:26:41,757 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2021-10-05 12:26:41,818 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits
2021-10-05 12:26:41,862 - stpipe.Detector1Pipeline.jump - INFO - Using 1 core for jump detection
2021-10-05 12:26:42,064 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-10-05 12:26:42,281 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-10-05 12:26:44,444 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 39308 pixels with at least one CR and at least four groups
2021-10-05 12:26:44,445 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 3301 pixels with at least one CR and three groups
2021-10-05 12:26:44,446 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 44253 pixels with at least one CR and two groups
2021-10-05 12:26:46,824 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 4.75849 sec
2021-10-05 12:26:46,828 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 5.084443
2021-10-05 12:26:46,831 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-10-05 12:26:47,023 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-10-05 12:26:47,025 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-10-05 12:26:47,068 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits
2021-10-05 12:26:47,118 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2021-10-05 12:26:47,179 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-10-05 12:26:47,181 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/jwst/ramp_fitting/ols_fit.py:1169: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int, :, :, :] *= (segs_4[num_int, :, :, :] > 0)
2021-10-05 12:27:14,076 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 6
2021-10-05 12:27:14,077 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-10-05 12:27:14,284 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-10-05 12:27:14,449 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-10-05 12:27:14,451 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:27:14,529 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-10-05 12:27:14,530 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-10-05 12:27:14,534 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:27:14,736 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-10-05 12:27:14,738 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:27:14,806 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-10-05 12:27:14,807 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-10-05 12:27:14,810 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:27:14,811 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-10-05 12:27:14,812 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-10-05 12:27:14,823 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:27:15,002 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-10-05 12:27:15,005 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
V8460001000101_msa.fits
2021-10-05 12:27:15,179 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2021-10-05 12:27:15,428 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-10-05 12:27:15,428 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-10-05 12:27:15,429 - stpipe.AssignWcsStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-10-05 12:27:15,430 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:27:15,626 - stpipe.AssignWcsStep - INFO - Removing slit 6 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,640 - stpipe.AssignWcsStep - INFO - Removing slit 7 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,654 - stpipe.AssignWcsStep - INFO - Removing slit 8 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,669 - stpipe.AssignWcsStep - INFO - Removing slit 9 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,683 - stpipe.AssignWcsStep - INFO - Removing slit 10 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,696 - stpipe.AssignWcsStep - INFO - Removing slit 11 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,710 - stpipe.AssignWcsStep - INFO - Removing slit 14 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,724 - stpipe.AssignWcsStep - INFO - Removing slit 15 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,738 - stpipe.AssignWcsStep - INFO - Removing slit 16 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,752 - stpipe.AssignWcsStep - INFO - Removing slit 17 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,766 - stpipe.AssignWcsStep - INFO - Removing slit 18 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,780 - stpipe.AssignWcsStep - INFO - Removing slit 19 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,793 - stpipe.AssignWcsStep - INFO - Removing slit 21 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,806 - stpipe.AssignWcsStep - INFO - Removing slit 25 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,819 - stpipe.AssignWcsStep - INFO - Removing slit 26 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,834 - stpipe.AssignWcsStep - INFO - Removing slit 27 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,848 - stpipe.AssignWcsStep - INFO - Removing slit 29 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,862 - stpipe.AssignWcsStep - INFO - Removing slit 31 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,876 - stpipe.AssignWcsStep - INFO - Removing slit 32 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,892 - stpipe.AssignWcsStep - INFO - Removing slit 33 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,906 - stpipe.AssignWcsStep - INFO - Removing slit 35 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,920 - stpipe.AssignWcsStep - INFO - Removing slit 37 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,934 - stpipe.AssignWcsStep - INFO - Removing slit 38 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,948 - stpipe.AssignWcsStep - INFO - Removing slit 39 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:15,963 - stpipe.AssignWcsStep - INFO - Removing slit 41 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,002 - stpipe.AssignWcsStep - INFO - Removing slit 1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,017 - stpipe.AssignWcsStep - INFO - Removing slit 2 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,032 - stpipe.AssignWcsStep - INFO - Removing slit 3 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,048 - stpipe.AssignWcsStep - INFO - Removing slit 4 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,063 - stpipe.AssignWcsStep - INFO - Removing slit 5 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,078 - stpipe.AssignWcsStep - INFO - Removing slit 12 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,093 - stpipe.AssignWcsStep - INFO - Removing slit 13 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,111 - stpipe.AssignWcsStep - INFO - Removing slit 20 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,126 - stpipe.AssignWcsStep - INFO - Removing slit 22 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,142 - stpipe.AssignWcsStep - INFO - Removing slit 23 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,160 - stpipe.AssignWcsStep - INFO - Removing slit 24 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,175 - stpipe.AssignWcsStep - INFO - Removing slit 28 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,191 - stpipe.AssignWcsStep - INFO - Removing slit 30 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,206 - stpipe.AssignWcsStep - INFO - Removing slit 34 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,222 - stpipe.AssignWcsStep - INFO - Removing slit 36 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,238 - stpipe.AssignWcsStep - INFO - Removing slit 40 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:16,569 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS1: [42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]
2021-10-05 12:27:16,570 - stpipe.AssignWcsStep - INFO - Computing WCS for 27 open slitlets
2021-10-05 12:27:16,599 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-10-05 12:27:16,600 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-10-05 12:27:16,601 - stpipe.AssignWcsStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-10-05 12:27:16,603 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:27:16,616 - stpipe.AssignWcsStep - INFO - SPORDER= -1, wrange=[9.7e-07, 1.89e-06]
2021-10-05 12:27:16,752 - stpipe.AssignWcsStep - INFO - There are 2 open slits in quadrant 1
2021-10-05 12:27:16,778 - stpipe.AssignWcsStep - INFO - There are 11 open slits in quadrant 2
2021-10-05 12:27:16,881 - stpipe.AssignWcsStep - INFO - There are 4 open slits in quadrant 3
2021-10-05 12:27:17,128 - stpipe.AssignWcsStep - INFO - There are 10 open slits in quadrant 4
2021-10-05 12:27:17,220 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 5
2021-10-05 12:27:17,378 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0032.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0023.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': 'V8460001000101_msa.fits'}
2021-10-05 12:27:18,126 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-10-05 12:27:18,134 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-10-05 12:27:18,146 - stpipe.MSAFlagOpenStep - INFO - MSAFlagOpenStep instance created.
2021-10-05 12:27:18,375 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-10-05 12:27:18,377 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-10-05 12:27:18,395 - stpipe.MSAFlagOpenStep - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2021-10-05 12:27:18,397 - stpipe.JwstStep - INFO - JwstStep instance created.
2021-10-05 12:27:18,529 - stpipe.MSAFlagOpenStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-10-05 12:27:18,531 - stpipe.MSAFlagOpenStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-10-05 12:27:18,532 - stpipe.MSAFlagOpenStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-10-05 12:27:18,534 - stpipe.MSAFlagOpenStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:27:18,546 - stpipe.MSAFlagOpenStep - INFO - SPORDER= -1, wrange=[9.7e-07, 1.89e-06]
2021-10-05 12:27:18,681 - stpipe.MSAFlagOpenStep - INFO - There are 5 open slits in quadrant 1
2021-10-05 12:27:18,726 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 2
2021-10-05 12:27:18,754 - stpipe.MSAFlagOpenStep - INFO - There are 9 open slits in quadrant 3
2021-10-05 12:27:18,829 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 4
2021-10-05 12:27:18,860 - stpipe.MSAFlagOpenStep - INFO - There are 0 open slits in quadrant 5
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-10-05 12:27:31,975 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep done
2021-10-05 12:27:32,793 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:27:32,803 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:27:33,181 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-10-05 12:27:33,184 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.45, 'slit_y_high': 0.45}
2021-10-05 12:27:33,341 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2021-10-05 12:27:33,403 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-10-05 12:27:33,404 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-10-05 12:27:33,406 - stpipe.AssignWcsStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-10-05 12:27:33,407 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:27:33,566 - stpipe.AssignWcsStep - INFO - Removing slit 1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:33,580 - stpipe.AssignWcsStep - INFO - Removing slit 2 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:33,634 - stpipe.AssignWcsStep - INFO - Removing slit 6 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:27:33,800 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS1: [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
2021-10-05 12:27:33,801 - stpipe.AssignWcsStep - INFO - Computing WCS for 16 open slitlets
2021-10-05 12:27:33,831 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-10-05 12:27:33,833 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-10-05 12:27:33,834 - stpipe.AssignWcsStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-10-05 12:27:33,835 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:27:33,845 - stpipe.AssignWcsStep - INFO - SPORDER= -1, wrange=[9.7e-07, 1.89e-06]
2021-10-05 12:27:33,968 - stpipe.AssignWcsStep - INFO - There are 3 open slits in quadrant 1
2021-10-05 12:27:33,999 - stpipe.AssignWcsStep - INFO - There are 2 open slits in quadrant 2
2021-10-05 12:27:34,018 - stpipe.AssignWcsStep - INFO - There are 9 open slits in quadrant 3
2021-10-05 12:27:34,100 - stpipe.AssignWcsStep - INFO - There are 2 open slits in quadrant 4
2021-10-05 12:27:34,122 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 5
2021-10-05 12:27:34,269 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0032.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0023.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': 'fopens_metafile_msa.fits'}
2021-10-05 12:27:34,846 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-10-05 12:27:34,853 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
Working with slit/slice: 3 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[1677 2048] [1630 1645]] Max value in slity array (ignoring NANs): 0.49983590702157094 percentage of F/O trace that was flagged: 99.8
Working with slit/slice: 4 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[1628 2048] [1320 1334]] Max value in slity array (ignoring NANs): 0.4999416262418918 percentage of F/O trace that was flagged: 99.8
Working with slit/slice: 5 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[1536 2048] [1591 1604]] Max value in slity array (ignoring NANs): 0.499395872247531 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 7 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[1531 2048] [ 239 251]] Max value in slity array (ignoring NANs): 0.49982577845792203 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 8 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[1510 2048] [ 163 175]] Max value in slity array (ignoring NANs): 0.4999363264129128 percentage of F/O trace that was flagged: 99.8
Working with slit/slice: 9 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[1114 2048] [1260 1273]] Max value in slity array (ignoring NANs): 0.49973662248892214 percentage of F/O trace that was flagged: 99.9
Working with slit/slice: 10 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[1113 2048] [1230 1243]] Max value in slity array (ignoring NANs): 0.499843929708657 percentage of F/O trace that was flagged: 99.9
Working with slit/slice: 11 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 881 2048] [1825 1841]] Max value in slity array (ignoring NANs): 0.49948331088759856 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 12 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 822 2048] [1249 1265]] Max value in slity array (ignoring NANs): 0.4997723843713606 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 13 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 622 2048] [1688 1708]] Max value in slity array (ignoring NANs): 0.4999716020776064 percentage of F/O trace that was flagged: 99.9
Working with slit/slice: 14 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 514 1982] [1628 1648]] Max value in slity array (ignoring NANs): 0.4997611753551952 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 15 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 386 1852] [1372 1394]] Max value in slity array (ignoring NANs): 0.49974517536774626 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 16 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 404 1873] [1856 1880]] Max value in slity array (ignoring NANs): 0.4997112322262246 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 17 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 385 1852] [1512 1534]] Max value in slity array (ignoring NANs): 0.4998204880532977 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 18 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 312 1773] [ 201 221]] Max value in slity array (ignoring NANs): 0.4999855029608435 percentage of F/O trace that was flagged: 99.9
Working with slit/slice: 19 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 282 1744] [ 619 640]] Max value in slity array (ignoring NANs): 0.49987583080741427 percentage of F/O trace that was flagged: 100.0
*** Final result for msa_flagging test will be reported as PASSED ***
('* MSA flagging validation test took ', '17.766819953918457 seconds to finish.')
Did msa_flagging validation test pass? True
Testing files for detector: nrs2
Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/mos_g140m_line1_NRS2_uncal.fits
2021-10-05 12:27:50,583 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-10-05 12:27:50,599 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-10-05 12:27:50,600 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-10-05 12:27:50,601 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-10-05 12:27:50,603 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-10-05 12:27:50,604 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-10-05 12:27:50,605 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-10-05 12:27:50,607 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-10-05 12:27:50,608 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-10-05 12:27:50,609 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-10-05 12:27:50,610 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-10-05 12:27:50,612 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-10-05 12:27:50,614 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-10-05 12:27:50,615 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-10-05 12:27:50,616 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-10-05 12:27:50,618 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-10-05 12:27:50,619 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-10-05 12:27:50,620 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/mos_g140m_line1_NRS2_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-10-05 12:27:50,843 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/mos_g140m_line1_NRS2_uncal.fits',).
2021-10-05 12:27:50,854 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-10-05 12:27:50,986 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'mos_g140m_line1_NRS2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-10-05 12:27:50,995 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0143.fits'.
2021-10-05 12:27:50,997 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits'.
2021-10-05 12:27:50,998 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0020.fits'.
2021-10-05 12:27:51,000 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0025.fits'.
2021-10-05 12:27:51,002 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-10-05 12:27:51,002 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0016.fits'.
2021-10-05 12:27:51,004 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2021-10-05 12:27:51,005 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-10-05 12:27:51,006 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-10-05 12:27:51,007 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0022.fits'.
2021-10-05 12:27:51,009 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0104.fits'.
2021-10-05 12:27:51,012 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-10-05 12:27:51,013 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-10-05 12:27:51,014 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-10-05 12:27:51,473 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-10-05 12:27:51,475 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:27:51,742 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-10-05 12:27:51,744 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-10-05 12:27:51,746 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-10-05 12:27:51,980 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-10-05 12:27:51,982 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:27:52,003 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0025.fits
2021-10-05 12:27:52,311 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-10-05 12:27:52,592 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-10-05 12:27:52,594 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:27:52,614 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0022.fits
2021-10-05 12:27:53,217 - stpipe.Detector1Pipeline.saturation - INFO - Detected 83201 saturated pixels
2021-10-05 12:27:53,251 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-10-05 12:27:53,262 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-10-05 12:27:53,534 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-10-05 12:27:53,536 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:27:53,537 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-10-05 12:27:53,539 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-10-05 12:27:53,792 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-10-05 12:27:53,794 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:27:53,817 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0104.fits
2021-10-05 12:27:54,126 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-10-05 12:27:54,430 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-10-05 12:27:54,432 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-10-05 12:27:54,442 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2021-10-05 12:27:54,443 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2021-10-05 12:27:54,444 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2021-10-05 12:27:54,444 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.000000
2021-10-05 12:27:54,445 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = True
2021-10-05 12:27:57,234 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-10-05 12:27:57,530 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-10-05 12:27:57,533 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:27:57,554 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0020.fits
2021-10-05 12:27:58,700 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-10-05 12:27:58,964 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-10-05 12:27:58,967 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'dark_output': None}
2021-10-05 12:27:58,988 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0143.fits
2021-10-05 12:27:59,274 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=6, nframes=1, groupgap=0
2021-10-05 12:27:59,275 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=10, nframes=1, groupgap=0
2021-10-05 12:27:59,608 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-10-05 12:27:59,881 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-10-05 12:27:59,883 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}
2021-10-05 12:27:59,893 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-10-05 12:27:59,905 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits
2021-10-05 12:27:59,977 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0016.fits
2021-10-05 12:28:00,030 - stpipe.Detector1Pipeline.jump - INFO - Using 1 core for jump detection
2021-10-05 12:28:00,278 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-10-05 12:28:00,539 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-10-05 12:28:02,959 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 39124 pixels with at least one CR and at least four groups
2021-10-05 12:28:02,960 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 2731 pixels with at least one CR and three groups
2021-10-05 12:28:02,961 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 48084 pixels with at least one CR and two groups
2021-10-05 12:28:05,947 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 5.66749 sec
2021-10-05 12:28:05,953 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 6.060817
2021-10-05 12:28:05,957 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-10-05 12:28:06,190 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-10-05 12:28:06,192 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-10-05 12:28:06,222 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0016.fits
2021-10-05 12:28:06,273 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits
2021-10-05 12:28:06,324 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-10-05 12:28:06,325 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/jwst/ramp_fitting/ols_fit.py:1169: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int, :, :, :] *= (segs_4[num_int, :, :, :] > 0)
2021-10-05 12:28:33,608 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 6
2021-10-05 12:28:33,609 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-10-05 12:28:33,818 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-10-05 12:28:33,992 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-10-05 12:28:33,994 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:28:34,067 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-10-05 12:28:34,068 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-10-05 12:28:34,070 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:28:34,197 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-10-05 12:28:34,199 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:28:34,263 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-10-05 12:28:34,264 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-10-05 12:28:34,267 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:28:34,268 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-10-05 12:28:34,270 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-10-05 12:28:34,279 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:28:34,407 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-10-05 12:28:34,409 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
V8460001000101_msa.fits
2021-10-05 12:28:34,567 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2021-10-05 12:28:34,798 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-10-05 12:28:34,799 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-10-05 12:28:34,800 - stpipe.AssignWcsStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-10-05 12:28:34,801 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:28:35,666 - stpipe.AssignWcsStep - INFO - Removing slit 65 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:35,683 - stpipe.AssignWcsStep - INFO - Removing slit 66 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:35,697 - stpipe.AssignWcsStep - INFO - Removing slit 68 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:35,735 - stpipe.AssignWcsStep - INFO - Removing slit 58 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:35,749 - stpipe.AssignWcsStep - INFO - Removing slit 59 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:35,763 - stpipe.AssignWcsStep - INFO - Removing slit 60 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:35,777 - stpipe.AssignWcsStep - INFO - Removing slit 61 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:35,791 - stpipe.AssignWcsStep - INFO - Removing slit 62 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:35,805 - stpipe.AssignWcsStep - INFO - Removing slit 63 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:35,818 - stpipe.AssignWcsStep - INFO - Removing slit 64 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:35,832 - stpipe.AssignWcsStep - INFO - Removing slit 67 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:35,833 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS2: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]
2021-10-05 12:28:35,834 - stpipe.AssignWcsStep - INFO - Computing WCS for 57 open slitlets
2021-10-05 12:28:35,863 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-10-05 12:28:35,864 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-10-05 12:28:35,865 - stpipe.AssignWcsStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-10-05 12:28:35,866 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:28:35,876 - stpipe.AssignWcsStep - INFO - SPORDER= -1, wrange=[9.7e-07, 1.89e-06]
2021-10-05 12:28:35,998 - stpipe.AssignWcsStep - INFO - There are 27 open slits in quadrant 1
2021-10-05 12:28:36,412 - stpipe.AssignWcsStep - INFO - There are 27 open slits in quadrant 2
2021-10-05 12:28:36,638 - stpipe.AssignWcsStep - INFO - There are 1 open slits in quadrant 3
2021-10-05 12:28:36,648 - stpipe.AssignWcsStep - INFO - There are 2 open slits in quadrant 4
2021-10-05 12:28:36,666 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 5
2021-10-05 12:28:36,819 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0032.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0023.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': 'V8460001000101_msa.fits'}
2021-10-05 12:28:37,829 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-10-05 12:28:37,836 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-10-05 12:28:37,845 - stpipe.MSAFlagOpenStep - INFO - MSAFlagOpenStep instance created.
2021-10-05 12:28:38,097 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-10-05 12:28:38,098 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-10-05 12:28:38,115 - stpipe.MSAFlagOpenStep - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2021-10-05 12:28:38,117 - stpipe.JwstStep - INFO - JwstStep instance created.
2021-10-05 12:28:38,241 - stpipe.MSAFlagOpenStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-10-05 12:28:38,242 - stpipe.MSAFlagOpenStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-10-05 12:28:38,243 - stpipe.MSAFlagOpenStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-10-05 12:28:38,244 - stpipe.MSAFlagOpenStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:28:38,254 - stpipe.MSAFlagOpenStep - INFO - SPORDER= -1, wrange=[9.7e-07, 1.89e-06]
2021-10-05 12:28:38,378 - stpipe.MSAFlagOpenStep - INFO - There are 5 open slits in quadrant 1
2021-10-05 12:28:38,424 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 2
2021-10-05 12:28:38,455 - stpipe.MSAFlagOpenStep - INFO - There are 9 open slits in quadrant 3
2021-10-05 12:28:38,534 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 4
2021-10-05 12:28:38,562 - stpipe.MSAFlagOpenStep - INFO - There are 0 open slits in quadrant 5
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-10-05 12:28:51,893 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep done
2021-10-05 12:28:52,633 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:28:52,644 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:28:53,144 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-10-05 12:28:53,147 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.45, 'slit_y_high': 0.45}
2021-10-05 12:28:53,293 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2021-10-05 12:28:53,345 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-10-05 12:28:53,346 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-10-05 12:28:53,347 - stpipe.AssignWcsStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-10-05 12:28:53,348 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:28:53,653 - stpipe.AssignWcsStep - INFO - Removing slit 13 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:53,667 - stpipe.AssignWcsStep - INFO - Removing slit 14 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:53,681 - stpipe.AssignWcsStep - INFO - Removing slit 15 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:53,695 - stpipe.AssignWcsStep - INFO - Removing slit 16 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:53,710 - stpipe.AssignWcsStep - INFO - Removing slit 17 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:53,724 - stpipe.AssignWcsStep - INFO - Removing slit 18 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:53,738 - stpipe.AssignWcsStep - INFO - Removing slit 19 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:28:53,739 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS2: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
2021-10-05 12:28:53,739 - stpipe.AssignWcsStep - INFO - Computing WCS for 12 open slitlets
2021-10-05 12:28:53,768 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-10-05 12:28:53,769 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-10-05 12:28:53,770 - stpipe.AssignWcsStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-10-05 12:28:53,772 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:28:53,782 - stpipe.AssignWcsStep - INFO - SPORDER= -1, wrange=[9.7e-07, 1.89e-06]
2021-10-05 12:28:53,908 - stpipe.AssignWcsStep - INFO - There are 5 open slits in quadrant 1
2021-10-05 12:28:53,953 - stpipe.AssignWcsStep - INFO - There are 3 open slits in quadrant 2
2021-10-05 12:28:53,983 - stpipe.AssignWcsStep - INFO - There are 4 open slits in quadrant 3
2021-10-05 12:28:54,019 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 4
2021-10-05 12:28:54,020 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 5
2021-10-05 12:28:54,151 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0032.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0023.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': 'fopens_metafile_msa.fits'}
2021-10-05 12:28:54,477 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-10-05 12:28:54,484 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
Working with slit/slice: 1 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 131 1613] [1906 1930]] Max value in slity array (ignoring NANs): 0.499879629054766 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 2 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 0 1330] [1823 1842]] Max value in slity array (ignoring NANs): 0.49995226747347604 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 3 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 0 957] [1631 1645]] Max value in slity array (ignoring NANs): 0.4997648773778204 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 4 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 0 906] [1320 1334]] Max value in slity array (ignoring NANs): 0.49972723641802796 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 5 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 0 814] [1591 1604]] Max value in slity array (ignoring NANs): 0.4997225330923289 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 6 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 50 1525] [ 680 699]] Max value in slity array (ignoring NANs): 0.49989116447537363 percentage of F/O trace that was flagged: 99.9
Working with slit/slice: 7 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 0 804] [239 251]] Max value in slity array (ignoring NANs): 0.49975066484744846 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 8 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 0 783] [163 175]] Max value in slity array (ignoring NANs): 0.49955175410051833 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 9 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 0 388] [1260 1273]] Max value in slity array (ignoring NANs): 0.4996146477571852 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 10 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 0 387] [1230 1243]] Max value in slity array (ignoring NANs): 0.4993629738181582 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 11 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 0 157] [1825 1841]] Max value in slity array (ignoring NANs): 0.35020493940891617 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 12 Slit min and max in y direction: -0.5 0.5 bounding box rounded to next integer: [[ 0 94] [1249 1265]] Max value in slity array (ignoring NANs): 0.4435073830894076 percentage of F/O trace that was flagged: 100.0
*** Final result for msa_flagging test will be reported as PASSED ***
('* MSA flagging validation test took ', '12.029757022857666 seconds to finish.')
Did msa_flagging validation test pass? True
Testing files for detector: nrs1
Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/ifu_prism_nrs1_uncal.fits
2021-10-05 12:29:04,982 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-10-05 12:29:04,998 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-10-05 12:29:04,999 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-10-05 12:29:05,001 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-10-05 12:29:05,002 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-10-05 12:29:05,003 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-10-05 12:29:05,005 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-10-05 12:29:05,006 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-10-05 12:29:05,007 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-10-05 12:29:05,009 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-10-05 12:29:05,010 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-10-05 12:29:05,011 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-10-05 12:29:05,012 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-10-05 12:29:05,013 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-10-05 12:29:05,015 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-10-05 12:29:05,016 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-10-05 12:29:05,018 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-10-05 12:29:05,019 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/ifu_prism_nrs1_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-10-05 12:29:05,255 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/ifu_prism_nrs1_uncal.fits',).
2021-10-05 12:29:05,265 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-10-05 12:29:05,400 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'ifu_prism_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-10-05 12:29:05,410 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0140.fits'.
2021-10-05 12:29:05,414 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits'.
2021-10-05 12:29:05,416 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits'.
2021-10-05 12:29:05,419 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0024.fits'.
2021-10-05 12:29:05,423 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-10-05 12:29:05,423 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits'.
2021-10-05 12:29:05,427 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2021-10-05 12:29:05,428 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-10-05 12:29:05,429 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-10-05 12:29:05,429 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits'.
2021-10-05 12:29:05,432 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0087.fits'.
2021-10-05 12:29:05,435 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-10-05 12:29:05,435 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-10-05 12:29:05,436 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-10-05 12:29:05,966 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-10-05 12:29:05,968 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:29:06,128 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-10-05 12:29:06,129 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-10-05 12:29:06,131 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-10-05 12:29:06,277 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-10-05 12:29:06,278 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:29:06,297 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0024.fits
2021-10-05 12:29:06,706 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-10-05 12:29:06,859 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-10-05 12:29:06,861 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:29:06,881 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits
2021-10-05 12:29:07,544 - stpipe.Detector1Pipeline.saturation - INFO - Detected 4320 saturated pixels
2021-10-05 12:29:07,602 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-10-05 12:29:07,611 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-10-05 12:29:07,773 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-10-05 12:29:07,777 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:29:07,778 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-10-05 12:29:07,781 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-10-05 12:29:07,933 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-10-05 12:29:07,934 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:29:07,954 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0087.fits
2021-10-05 12:29:08,265 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-10-05 12:29:08,417 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-10-05 12:29:08,418 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-10-05 12:29:08,427 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2021-10-05 12:29:08,428 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2021-10-05 12:29:08,428 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2021-10-05 12:29:08,429 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.000000
2021-10-05 12:29:08,430 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = True
2021-10-05 12:29:12,106 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-10-05 12:29:12,278 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-10-05 12:29:12,280 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:29:12,302 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits
2021-10-05 12:29:13,473 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-10-05 12:29:13,628 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-10-05 12:29:13,629 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'dark_output': None}
2021-10-05 12:29:13,648 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0140.fits
2021-10-05 12:29:13,889 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=10, nframes=1, groupgap=0
2021-10-05 12:29:13,890 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=10, nframes=1, groupgap=0
2021-10-05 12:29:14,234 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-10-05 12:29:14,429 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-10-05 12:29:14,431 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}
2021-10-05 12:29:14,440 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-10-05 12:29:14,451 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2021-10-05 12:29:14,509 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits
2021-10-05 12:29:14,551 - stpipe.Detector1Pipeline.jump - INFO - Using 1 core for jump detection
2021-10-05 12:29:14,837 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-10-05 12:29:15,224 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-10-05 12:29:18,197 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 75673 pixels with at least one CR and at least four groups
2021-10-05 12:29:18,198 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 4 pixels with at least one CR and three groups
2021-10-05 12:29:18,198 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 4093 pixels with at least one CR and two groups
2021-10-05 12:29:20,327 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 5.48892 sec
2021-10-05 12:29:20,330 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 5.890422
2021-10-05 12:29:20,333 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-10-05 12:29:20,484 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-10-05 12:29:20,486 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-10-05 12:29:20,515 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits
2021-10-05 12:29:20,558 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2021-10-05 12:29:20,603 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-10-05 12:29:20,604 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/jwst/ramp_fitting/ols_fit.py:1169: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int, :, :, :] *= (segs_4[num_int, :, :, :] > 0)
2021-10-05 12:30:09,359 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 10
2021-10-05 12:30:09,360 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-10-05 12:30:09,657 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-10-05 12:30:09,883 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-10-05 12:30:09,885 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:30:10,010 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-10-05 12:30:10,011 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-10-05 12:30:10,014 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:30:10,188 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-10-05 12:30:10,190 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:30:10,257 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-10-05 12:30:10,258 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-10-05 12:30:10,260 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:30:10,262 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-10-05 12:30:10,263 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-10-05 12:30:10,274 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:30:10,445 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-10-05 12:30:10,447 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2021-10-05 12:30:10,654 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.03312480077147484 deg
2021-10-05 12:30:10,655 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3411945700645447 deg
2021-10-05 12:30:10,656 - stpipe.AssignWcsStep - INFO - theta_y correction: -0.005294283663966503 deg
2021-10-05 12:30:10,657 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:30:14,290 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_ifu pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0034.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0028.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': '/grp/crds/cache/references/jwst/jwst_nirspec_ifupost_0004.asdf', 'ifufore': '/grp/crds/cache/references/jwst/jwst_nirspec_ifufore_0003.asdf', 'ifuslicer': '/grp/crds/cache/references/jwst/jwst_nirspec_ifuslicer_0003.asdf'}
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-10-05 12:30:19,890 - stpipe.AssignWcsStep - INFO - Update S_REGION to POLYGON ICRS 156.176998032 -45.687618307 156.178780407 -45.687618307 156.178780407 -45.686330486 156.176998032 -45.686330486
2021-10-05 12:30:19,893 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-10-05 12:30:19,904 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-10-05 12:30:19,919 - stpipe.MSAFlagOpenStep - INFO - MSAFlagOpenStep instance created.
2021-10-05 12:30:20,300 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-10-05 12:30:20,303 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-10-05 12:30:20,331 - stpipe.MSAFlagOpenStep - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2021-10-05 12:30:20,332 - stpipe.JwstStep - INFO - JwstStep instance created.
2021-10-05 12:30:20,453 - stpipe.MSAFlagOpenStep - INFO - gwa_ytilt is 0.03312480077147484 deg
2021-10-05 12:30:20,454 - stpipe.MSAFlagOpenStep - INFO - gwa_xtilt is 0.3411945700645447 deg
2021-10-05 12:30:20,455 - stpipe.MSAFlagOpenStep - INFO - theta_y correction: -0.005294283663966503 deg
2021-10-05 12:30:20,456 - stpipe.MSAFlagOpenStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:30:20,467 - stpipe.MSAFlagOpenStep - INFO - SPORDER= 0, wrange=[6e-07, 5.3e-06]
2021-10-05 12:30:20,591 - stpipe.MSAFlagOpenStep - INFO - There are 5 open slits in quadrant 1
2021-10-05 12:30:20,636 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 2
2021-10-05 12:30:20,665 - stpipe.MSAFlagOpenStep - INFO - There are 9 open slits in quadrant 3
2021-10-05 12:30:20,746 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 4
2021-10-05 12:30:20,775 - stpipe.MSAFlagOpenStep - INFO - There are 0 open slits in quadrant 5
2021-10-05 12:30:35,896 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep done
2021-10-05 12:30:37,097 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:30:37,109 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:30:37,861 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-10-05 12:30:37,864 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.45, 'slit_y_high': 0.45}
2021-10-05 12:30:38,033 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2021-10-05 12:30:38,089 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.03312480077147484 deg
2021-10-05 12:30:38,090 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3411945700645447 deg
2021-10-05 12:30:38,091 - stpipe.AssignWcsStep - INFO - theta_y correction: -0.005294283663966503 deg
2021-10-05 12:30:38,092 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:30:38,304 - stpipe.AssignWcsStep - INFO - Removing slit 1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:30:38,352 - stpipe.AssignWcsStep - INFO - Removing slit 2 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:30:38,551 - stpipe.AssignWcsStep - INFO - Removing slit 6 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:30:38,632 - stpipe.AssignWcsStep - INFO - Removing slit 7 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:30:38,682 - stpipe.AssignWcsStep - INFO - Removing slit 8 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:30:39,229 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS1: [3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
2021-10-05 12:30:39,230 - stpipe.AssignWcsStep - INFO - Computing WCS for 14 open slitlets
2021-10-05 12:30:39,270 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.03312480077147484 deg
2021-10-05 12:30:39,271 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3411945700645447 deg
2021-10-05 12:30:39,272 - stpipe.AssignWcsStep - INFO - theta_y correction: -0.005294283663966503 deg
2021-10-05 12:30:39,273 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:30:39,284 - stpipe.AssignWcsStep - INFO - SPORDER= 0, wrange=[6e-07, 5.3e-06]
2021-10-05 12:30:39,419 - stpipe.AssignWcsStep - INFO - There are 3 open slits in quadrant 1
2021-10-05 12:30:39,451 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 2
2021-10-05 12:30:39,452 - stpipe.AssignWcsStep - INFO - There are 9 open slits in quadrant 3
2021-10-05 12:30:39,538 - stpipe.AssignWcsStep - INFO - There are 2 open slits in quadrant 4
2021-10-05 12:30:39,558 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 5
2021-10-05 12:30:39,698 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0034.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0028.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': 'fopens_metafile_msa.fits'}
2021-10-05 12:30:40,039 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-10-05 12:30:40,047 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
Working with slit/slice: 3 bounding box rounded to next integer: [[2004 2048] [1629 1641]] Max value in slity array (ignoring NANs): 0.4996944183018942 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 4 bounding box rounded to next integer: [[2015 2048] [1319 1331]] Max value in slity array (ignoring NANs): 0.499662912467855 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 5 bounding box rounded to next integer: [[1870 2048] [1590 1601]] Max value in slity array (ignoring NANs): 0.4999703890806265 percentage of F/O trace that was flagged: 99.5
Working with slit/slice: 9 bounding box rounded to next integer: [[1508 1936] [1261 1271]] Max value in slity array (ignoring NANs): 0.4710906044496709 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 10 bounding box rounded to next integer: [[1512 1940] [1230 1241]] Max value in slity array (ignoring NANs): 0.4998853904086488 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 11 bounding box rounded to next integer: [[1157 1591] [1827 1837]] Max value in slity array (ignoring NANs): 0.49874262416463067 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 12 bounding box rounded to next integer: [[1210 1640] [1251 1261]] Max value in slity array (ignoring NANs): 0.4911423826049948 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 13 bounding box rounded to next integer: [[ 917 1353] [1692 1703]] Max value in slity array (ignoring NANs): 0.4999315450304109 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 14 bounding box rounded to next integer: [[ 816 1253] [1632 1643]] Max value in slity array (ignoring NANs): 0.4993213221807147 percentage of F/O trace that was flagged: 99.8
Working with slit/slice: 15 bounding box rounded to next integer: [[ 733 1169] [1376 1388]] Max value in slity array (ignoring NANs): 0.4995603819332174 percentage of F/O trace that was flagged: 99.8
Working with slit/slice: 16 bounding box rounded to next integer: [[ 653 1093] [1862 1874]] Max value in slity array (ignoring NANs): 0.49887079905583886 percentage of F/O trace that was flagged: 99.8
Working with slit/slice: 17 bounding box rounded to next integer: [[ 704 1141] [1517 1528]] Max value in slity array (ignoring NANs): 0.4998723633645087 percentage of F/O trace that was flagged: 99.8
Working with slit/slice: 18 bounding box rounded to next integer: [[ 856 1284] [ 205 215]] Max value in slity array (ignoring NANs): 0.4991210494201372 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 19 bounding box rounded to next integer: [[ 758 1190] [ 623 634]] Max value in slity array (ignoring NANs): 0.49985430663769975 percentage of F/O trace that was flagged: 99.8
*** Final result for msa_flagging test will be reported as PASSED ***
('* MSA flagging validation test took ', '18.75812792778015 seconds to finish.')
Did msa_flagging validation test pass? True
Testing files for detector: nrs2
Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/ifu_prism_nrs2_uncal.fits
2021-10-05 12:30:56,059 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-10-05 12:30:56,076 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-10-05 12:30:56,078 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-10-05 12:30:56,080 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-10-05 12:30:56,081 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-10-05 12:30:56,082 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-10-05 12:30:56,084 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-10-05 12:30:56,085 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-10-05 12:30:56,086 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-10-05 12:30:56,088 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-10-05 12:30:56,089 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-10-05 12:30:56,091 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-10-05 12:30:56,092 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-10-05 12:30:56,094 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-10-05 12:30:56,095 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-10-05 12:30:56,097 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-10-05 12:30:56,098 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-10-05 12:30:56,100 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/ifu_prism_nrs2_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-10-05 12:30:56,443 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/ifu_prism_nrs2_uncal.fits',).
2021-10-05 12:30:56,454 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-10-05 12:30:56,615 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'ifu_prism_nrs2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-10-05 12:30:56,624 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0143.fits'.
2021-10-05 12:30:56,625 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits'.
2021-10-05 12:30:56,627 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0021.fits'.
2021-10-05 12:30:56,628 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0025.fits'.
2021-10-05 12:30:56,630 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-10-05 12:30:56,630 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0016.fits'.
2021-10-05 12:30:56,632 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2021-10-05 12:30:56,632 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-10-05 12:30:56,633 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-10-05 12:30:56,633 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0021.fits'.
2021-10-05 12:30:56,635 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0104.fits'.
2021-10-05 12:30:56,636 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-10-05 12:30:56,637 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-10-05 12:30:56,638 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-10-05 12:30:57,138 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-10-05 12:30:57,139 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:30:57,310 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-10-05 12:30:57,312 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-10-05 12:30:57,313 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-10-05 12:30:57,501 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-10-05 12:30:57,503 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:30:57,523 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0025.fits
2021-10-05 12:30:57,902 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-10-05 12:30:58,091 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-10-05 12:30:58,093 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:30:58,113 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0021.fits
2021-10-05 12:30:58,752 - stpipe.Detector1Pipeline.saturation - INFO - Detected 2388 saturated pixels
2021-10-05 12:30:58,793 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-10-05 12:30:58,802 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-10-05 12:30:58,988 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-10-05 12:30:58,990 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:30:58,990 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-10-05 12:30:58,992 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-10-05 12:30:59,176 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-10-05 12:30:59,178 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:30:59,198 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0104.fits
2021-10-05 12:30:59,562 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-10-05 12:30:59,750 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-10-05 12:30:59,752 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-10-05 12:30:59,760 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2021-10-05 12:30:59,761 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2021-10-05 12:30:59,761 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2021-10-05 12:30:59,762 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.000000
2021-10-05 12:30:59,762 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = True
2021-10-05 12:31:03,225 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-10-05 12:31:03,418 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-10-05 12:31:03,420 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:31:03,440 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0021.fits
2021-10-05 12:31:04,412 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-10-05 12:31:04,590 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-10-05 12:31:04,592 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'dark_output': None}
2021-10-05 12:31:04,611 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0143.fits
2021-10-05 12:31:04,862 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=10, nframes=1, groupgap=0
2021-10-05 12:31:04,863 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=10, nframes=1, groupgap=0
2021-10-05 12:31:05,174 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-10-05 12:31:05,363 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-10-05 12:31:05,365 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}
2021-10-05 12:31:05,373 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-10-05 12:31:05,386 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits
2021-10-05 12:31:05,446 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0016.fits
2021-10-05 12:31:05,491 - stpipe.Detector1Pipeline.jump - INFO - Using 1 core for jump detection
2021-10-05 12:31:05,761 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-10-05 12:31:06,092 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-10-05 12:31:08,870 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 28387 pixels with at least one CR and at least four groups
2021-10-05 12:31:08,871 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 0 pixels with at least one CR and three groups
2021-10-05 12:31:08,871 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 2294 pixels with at least one CR and two groups
2021-10-05 12:31:09,897 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 4.13467 sec
2021-10-05 12:31:09,900 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 4.526673
2021-10-05 12:31:09,903 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-10-05 12:31:10,096 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-10-05 12:31:10,098 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-10-05 12:31:10,134 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0016.fits
2021-10-05 12:31:10,180 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits
2021-10-05 12:31:10,227 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-10-05 12:31:10,228 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/jwst/ramp_fitting/ols_fit.py:1169: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int, :, :, :] *= (segs_4[num_int, :, :, :] > 0)
2021-10-05 12:31:52,262 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 10
2021-10-05 12:31:52,264 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-10-05 12:31:52,501 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-10-05 12:31:52,705 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-10-05 12:31:52,707 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:31:52,776 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-10-05 12:31:52,777 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-10-05 12:31:52,779 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:31:52,965 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-10-05 12:31:52,967 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:31:53,041 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-10-05 12:31:53,043 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-10-05 12:31:53,045 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:31:53,047 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-10-05 12:31:53,048 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-10-05 12:31:53,059 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:31:53,255 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-10-05 12:31:53,257 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2021-10-05 12:31:53,439 - stpipe.AssignWcsStep - CRITICAL - No IFU slices fall on detector NRS2
An error occured with AssignWcs. Likely: No open slits fall on detector nrs2 Skipping test for this file. Did msa_flagging validation test pass? skipped Testing files for detector: nrs1 Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/ifu_g395h_f290lp_nrs1_uncal.fits
2021-10-05 12:31:55,901 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-10-05 12:31:55,916 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-10-05 12:31:55,918 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-10-05 12:31:55,919 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-10-05 12:31:55,920 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-10-05 12:31:55,921 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-10-05 12:31:55,923 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-10-05 12:31:55,924 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-10-05 12:31:55,925 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-10-05 12:31:55,926 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-10-05 12:31:55,927 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-10-05 12:31:55,928 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-10-05 12:31:55,929 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-10-05 12:31:55,930 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-10-05 12:31:55,931 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-10-05 12:31:55,933 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-10-05 12:31:55,934 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-10-05 12:31:55,936 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/ifu_g395h_f290lp_nrs1_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-10-05 12:31:56,156 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/ifu_g395h_f290lp_nrs1_uncal.fits',).
2021-10-05 12:31:56,166 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-10-05 12:31:56,462 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'ifu_g395h_f290lp_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-10-05 12:31:56,471 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0088.fits'.
2021-10-05 12:31:56,473 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0023.fits'.
2021-10-05 12:31:56,474 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0022.fits'.
2021-10-05 12:31:56,476 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits'.
2021-10-05 12:31:56,477 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-10-05 12:31:56,478 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits'.
2021-10-05 12:31:56,479 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_refpix_0019.fits'.
2021-10-05 12:31:56,481 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-10-05 12:31:56,481 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-10-05 12:31:56,482 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0027.fits'.
2021-10-05 12:31:56,483 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0117.fits'.
2021-10-05 12:31:56,485 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-10-05 12:31:56,485 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-10-05 12:31:56,486 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-10-05 12:31:57,553 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-10-05 12:31:57,555 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:31:58,351 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-10-05 12:31:58,353 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-10-05 12:31:58,356 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-10-05 12:31:58,534 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-10-05 12:31:58,536 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:31:58,556 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits
2021-10-05 12:31:59,533 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-10-05 12:31:59,788 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-10-05 12:31:59,790 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:31:59,810 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0027.fits
2021-10-05 12:32:02,112 - stpipe.Detector1Pipeline.saturation - INFO - Detected 131958 saturated pixels
2021-10-05 12:32:02,230 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-10-05 12:32:02,251 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-10-05 12:32:02,504 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-10-05 12:32:02,506 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:32:02,506 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-10-05 12:32:02,508 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-10-05 12:32:02,687 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-10-05 12:32:02,689 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:32:02,709 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0117.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stdatamodels/validate.py:34: ValidationWarning: While validating meta.exposure.readpatt the following error occurred:
'ALLIRS2' is not one of ['ACQ1', 'ACQ2', 'BRIGHT1', 'BRIGHT2', 'DEEP2', 'DEEP8', 'FAST', 'FASTGRPAVG', 'FASTGRPAVG8', 'FASTGRPAVG16', 'FASTGRPAVG32', 'FASTGRPAVG64', 'FASTR1', 'FASTR100', 'FGS', 'FGS60', 'FGS8370', 'FGS840', 'FGSRAPID', 'FINEGUIDE', 'ID', 'MEDIUM2', 'MEDIUM8', 'NIS', 'NISRAPID', 'NRS', 'NRSIRS2', 'NRSN16R4', 'NRSN32R8', 'NRSN8R2', 'NRSRAPID', 'NRSIRS2RAPID', 'NRSRAPIDD1', 'NRSRAPIDD2', 'NRSRAPIDD6', 'NRSSLOW', 'RAPID', 'SHALLOW2', 'SHALLOW4', 'SLOW', 'SLOWR1', 'TRACK', 'ANY', 'N/A']
Failed validating 'enum' in schema:
OrderedDict([('title', 'Readout pattern'),
('type', 'string'),
('enum',
['ACQ1',
'ACQ2',
'BRIGHT1',
'BRIGHT2',
'DEEP2',
'DEEP8',
'FAST',
'FASTGRPAVG',
'FASTGRPAVG8',
'FASTGRPAVG16',
'FASTGRPAVG32',
'FASTGRPAVG64',
'FASTR1',
'FASTR100',
'FGS',
'FGS60',
'FGS8370',
'FGS840',
'FGSRAPID',
'FINEGUIDE',
'ID',
'MEDIUM2',
'MEDIUM8',
'NIS',
'NISRAPID',
'NRS',
'NRSIRS2',
'NRSN16R4',
'NRSN32R8',
'NRSN8R2',
'NRSRAPID',
'NRSIRS2RAPID',
'NRSRAPIDD1',
'NRSRAPIDD2',
'NRSRAPIDD6',
'NRSSLOW',
'RAPID',
'SHALLOW2',
'SHALLOW4',
'SLOW',
'SLOWR1',
'TRACK',
'ANY',
'N/A']),
('fits_ke ...
warnings.warn(errmsg, ValidationWarning)
2021-10-05 12:32:03,888 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-10-05 12:32:04,151 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-10-05 12:32:04,152 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-10-05 12:32:04,173 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /grp/crds/cache/references/jwst/jwst_nirspec_refpix_0019.fits
2021-10-05 12:33:10,951 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-10-05 12:33:11,323 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-10-05 12:33:11,325 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:33:11,352 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0022.fits
2021-10-05 12:33:11,487 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2021-10-05 12:33:13,266 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-10-05 12:33:13,549 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-10-05 12:33:13,551 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'dark_output': None}
2021-10-05 12:33:13,992 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0088.fits
2021-10-05 12:33:18,225 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=20, nframes=1, groupgap=0
2021-10-05 12:33:18,226 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=65, nframes=1, groupgap=0
2021-10-05 12:33:20,009 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-10-05 12:33:20,745 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-10-05 12:33:20,747 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}
2021-10-05 12:33:20,880 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-10-05 12:33:21,146 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0023.fits
2021-10-05 12:33:21,435 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2021-10-05 12:33:21,488 - stpipe.Detector1Pipeline.jump - INFO - Using 1 core for jump detection
2021-10-05 12:33:22,547 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-10-05 12:33:23,244 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-10-05 12:33:28,366 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 96703 pixels with at least one CR and at least four groups
2021-10-05 12:33:28,367 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 406 pixels with at least one CR and three groups
2021-10-05 12:33:28,368 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 27166 pixels with at least one CR and two groups
2021-10-05 12:33:36,447 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 13.8987 sec
2021-10-05 12:33:36,450 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 15.570088
2021-10-05 12:33:36,453 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-10-05 12:33:36,853 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-10-05 12:33:36,855 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-10-05 12:33:37,395 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2021-10-05 12:33:37,444 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0023.fits
2021-10-05 12:33:37,468 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-10-05 12:33:37,469 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/jwst/ramp_fitting/ols_fit.py:1169: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int, :, :, :] *= (segs_4[num_int, :, :, :] > 0)
2021-10-05 12:36:24,282 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 20
2021-10-05 12:36:24,283 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-10-05 12:36:24,557 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-10-05 12:36:24,950 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-10-05 12:36:24,953 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:36:25,010 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2021-10-05 12:36:25,023 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:36:25,192 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-10-05 12:36:25,194 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:36:25,249 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2021-10-05 12:36:25,262 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:36:25,264 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-10-05 12:36:25,265 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-10-05 12:36:25,277 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:36:25,531 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-10-05 12:36:25,533 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2021-10-05 12:36:25,731 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-10-05 12:36:25,733 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-10-05 12:36:25,734 - stpipe.AssignWcsStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-10-05 12:36:25,735 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:36:29,350 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_ifu pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0035.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0022.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': '/grp/crds/cache/references/jwst/jwst_nirspec_ifupost_0004.asdf', 'ifufore': '/grp/crds/cache/references/jwst/jwst_nirspec_ifufore_0003.asdf', 'ifuslicer': '/grp/crds/cache/references/jwst/jwst_nirspec_ifuslicer_0003.asdf'}
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-10-05 12:36:36,283 - stpipe.AssignWcsStep - INFO - Update S_REGION to POLYGON ICRS 156.176999392 -45.687618156 156.178775679 -45.687618156 156.178775679 -45.686331563 156.176999392 -45.686331563
2021-10-05 12:36:36,284 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-10-05 12:36:36,291 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-10-05 12:36:36,301 - stpipe.MSAFlagOpenStep - INFO - MSAFlagOpenStep instance created.
2021-10-05 12:36:36,661 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-10-05 12:36:36,664 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-10-05 12:36:36,683 - stpipe.MSAFlagOpenStep - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2021-10-05 12:36:36,685 - stpipe.JwstStep - INFO - JwstStep instance created.
2021-10-05 12:36:36,807 - stpipe.MSAFlagOpenStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-10-05 12:36:36,808 - stpipe.MSAFlagOpenStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-10-05 12:36:36,809 - stpipe.MSAFlagOpenStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-10-05 12:36:36,810 - stpipe.MSAFlagOpenStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:36:36,820 - stpipe.MSAFlagOpenStep - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2021-10-05 12:36:36,943 - stpipe.MSAFlagOpenStep - INFO - There are 5 open slits in quadrant 1
2021-10-05 12:36:36,988 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 2
2021-10-05 12:36:37,016 - stpipe.MSAFlagOpenStep - INFO - There are 9 open slits in quadrant 3
2021-10-05 12:36:37,095 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 4
2021-10-05 12:36:37,125 - stpipe.MSAFlagOpenStep - INFO - There are 0 open slits in quadrant 5
2021-10-05 12:36:51,093 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep done
2021-10-05 12:36:51,827 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:36:51,838 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:36:52,590 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-10-05 12:36:52,593 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.45, 'slit_y_high': 0.45}
2021-10-05 12:36:52,748 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2021-10-05 12:36:52,798 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-10-05 12:36:52,799 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-10-05 12:36:52,800 - stpipe.AssignWcsStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-10-05 12:36:52,801 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:36:52,966 - stpipe.AssignWcsStep - INFO - Removing slit 1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:36:52,988 - stpipe.AssignWcsStep - INFO - Removing slit 2 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:36:53,073 - stpipe.AssignWcsStep - INFO - Removing slit 6 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-10-05 12:36:53,340 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS1: [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
2021-10-05 12:36:53,341 - stpipe.AssignWcsStep - INFO - Computing WCS for 16 open slitlets
2021-10-05 12:36:53,370 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-10-05 12:36:53,371 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-10-05 12:36:53,372 - stpipe.AssignWcsStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-10-05 12:36:53,373 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:36:53,383 - stpipe.AssignWcsStep - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2021-10-05 12:36:53,501 - stpipe.AssignWcsStep - INFO - There are 3 open slits in quadrant 1
2021-10-05 12:36:53,530 - stpipe.AssignWcsStep - INFO - There are 2 open slits in quadrant 2
2021-10-05 12:36:53,548 - stpipe.AssignWcsStep - INFO - There are 9 open slits in quadrant 3
2021-10-05 12:36:53,625 - stpipe.AssignWcsStep - INFO - There are 2 open slits in quadrant 4
2021-10-05 12:36:53,644 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 5
2021-10-05 12:36:53,775 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0035.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0022.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': 'fopens_metafile_msa.fits'}
2021-10-05 12:36:54,105 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-10-05 12:36:54,112 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
Working with slit/slice: 3 bounding box rounded to next integer: [[1859 2048] [1638 1710]] Max value in slity array (ignoring NANs): 0.39354276760554147 percentage of F/O trace that was flagged: 99.6
Working with slit/slice: 4 bounding box rounded to next integer: [[1794 2048] [1328 1392]] Max value in slity array (ignoring NANs): 0.36978689638762896 percentage of F/O trace that was flagged: 99.6
Working with slit/slice: 5 bounding box rounded to next integer: [[1716 2048] [1598 1663]] Max value in slity array (ignoring NANs): 0.4996419343238408 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 7 bounding box rounded to next integer: [[1648 2048] [ 246 292]] Max value in slity array (ignoring NANs): 0.4998979465523029 percentage of F/O trace that was flagged: 99.7
Working with slit/slice: 8 bounding box rounded to next integer: [[1625 2048] [ 171 215]] Max value in slity array (ignoring NANs): 0.4914901689090161 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 9 bounding box rounded to next integer: [[1278 2048] [1267 1312]] Max value in slity array (ignoring NANs): 0.49972222654550663 percentage of F/O trace that was flagged: 99.9
Working with slit/slice: 10 bounding box rounded to next integer: [[1276 2048] [1237 1282]] Max value in slity array (ignoring NANs): 0.49974965593991627 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 11 bounding box rounded to next integer: [[1076 2048] [1832 1876]] Max value in slity array (ignoring NANs): 0.4995125587178428 percentage of F/O trace that was flagged: 99.9
Working with slit/slice: 12 bounding box rounded to next integer: [[ 987 2048] [1256 1293]] Max value in slity array (ignoring NANs): 0.4998321968363724 percentage of F/O trace that was flagged: 99.9
Working with slit/slice: 13 bounding box rounded to next integer: [[ 812 2048] [1695 1731]] Max value in slity array (ignoring NANs): 0.4997389937798961 percentage of F/O trace that was flagged: 99.9
Working with slit/slice: 14 bounding box rounded to next integer: [[ 702 2048] [1635 1667]] Max value in slity array (ignoring NANs): 0.49993406575349 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 15 bounding box rounded to next integer: [[ 562 2048] [1379 1407]] Max value in slity array (ignoring NANs): 0.4999204166968889 percentage of F/O trace that was flagged: 99.9
Working with slit/slice: 16 bounding box rounded to next integer: [[ 606 2048] [1863 1895]] Max value in slity array (ignoring NANs): 0.4997743958906472 percentage of F/O trace that was flagged: 99.9
Working with slit/slice: 17 bounding box rounded to next integer: [[ 568 2048] [1519 1547]] Max value in slity array (ignoring NANs): 0.4999226887144772 percentage of F/O trace that was flagged: 99.9
Working with slit/slice: 18 bounding box rounded to next integer: [[ 437 2048] [ 208 229]] Max value in slity array (ignoring NANs): 0.4999158219759617 percentage of F/O trace that was flagged: 99.9
Working with slit/slice: 19 bounding box rounded to next integer: [[ 424 2048] [ 626 648]] Max value in slity array (ignoring NANs): 0.49974363642795727 percentage of F/O trace that was flagged: 99.9
*** Final result for msa_flagging test will be reported as PASSED ***
('* MSA flagging validation test took ', '18.321805953979492 seconds to finish.')
Did msa_flagging validation test pass? True
Testing files for detector: nrs2
Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/ifu_g395h_f290lp_nrs2_uncal.fits
2021-10-05 12:37:11,709 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-10-05 12:37:11,727 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-10-05 12:37:11,729 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-10-05 12:37:11,730 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-10-05 12:37:11,731 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-10-05 12:37:11,733 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-10-05 12:37:11,734 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-10-05 12:37:11,735 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-10-05 12:37:11,737 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-10-05 12:37:11,738 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-10-05 12:37:11,739 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-10-05 12:37:11,740 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-10-05 12:37:11,741 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-10-05 12:37:11,743 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-10-05 12:37:11,744 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-10-05 12:37:11,745 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-10-05 12:37:11,746 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-10-05 12:37:11,748 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/ifu_g395h_f290lp_nrs2_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-10-05 12:37:12,169 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5/ifu_g395h_f290lp_nrs2_uncal.fits',).
2021-10-05 12:37:12,180 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-10-05 12:37:12,445 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'ifu_g395h_f290lp_nrs2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-10-05 12:37:12,456 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0085.fits'.
2021-10-05 12:37:12,459 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0020.fits'.
2021-10-05 12:37:12,463 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0025.fits'.
2021-10-05 12:37:12,466 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0011.fits'.
2021-10-05 12:37:12,469 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-10-05 12:37:12,470 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits'.
2021-10-05 12:37:12,473 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_refpix_0018.fits'.
2021-10-05 12:37:12,475 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-10-05 12:37:12,476 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-10-05 12:37:12,477 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0026.fits'.
2021-10-05 12:37:12,480 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0118.fits'.
2021-10-05 12:37:12,483 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-10-05 12:37:12,484 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-10-05 12:37:12,484 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-10-05 12:37:13,505 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-10-05 12:37:13,507 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:37:14,312 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-10-05 12:37:14,313 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-10-05 12:37:14,315 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-10-05 12:37:14,490 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-10-05 12:37:14,492 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:37:14,512 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0011.fits
2021-10-05 12:37:15,512 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-10-05 12:37:15,771 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-10-05 12:37:15,773 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:37:15,792 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0026.fits
2021-10-05 12:37:18,077 - stpipe.Detector1Pipeline.saturation - INFO - Detected 151502 saturated pixels
2021-10-05 12:37:18,214 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-10-05 12:37:18,235 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-10-05 12:37:18,500 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-10-05 12:37:18,502 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:37:18,503 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-10-05 12:37:18,504 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-10-05 12:37:18,688 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-10-05 12:37:18,690 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:37:18,711 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0118.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stdatamodels/validate.py:34: ValidationWarning: While validating meta.exposure.readpatt the following error occurred:
'ALLIRS2' is not one of ['ACQ1', 'ACQ2', 'BRIGHT1', 'BRIGHT2', 'DEEP2', 'DEEP8', 'FAST', 'FASTGRPAVG', 'FASTGRPAVG8', 'FASTGRPAVG16', 'FASTGRPAVG32', 'FASTGRPAVG64', 'FASTR1', 'FASTR100', 'FGS', 'FGS60', 'FGS8370', 'FGS840', 'FGSRAPID', 'FINEGUIDE', 'ID', 'MEDIUM2', 'MEDIUM8', 'NIS', 'NISRAPID', 'NRS', 'NRSIRS2', 'NRSN16R4', 'NRSN32R8', 'NRSN8R2', 'NRSRAPID', 'NRSIRS2RAPID', 'NRSRAPIDD1', 'NRSRAPIDD2', 'NRSRAPIDD6', 'NRSSLOW', 'RAPID', 'SHALLOW2', 'SHALLOW4', 'SLOW', 'SLOWR1', 'TRACK', 'ANY', 'N/A']
Failed validating 'enum' in schema:
OrderedDict([('title', 'Readout pattern'),
('type', 'string'),
('enum',
['ACQ1',
'ACQ2',
'BRIGHT1',
'BRIGHT2',
'DEEP2',
'DEEP8',
'FAST',
'FASTGRPAVG',
'FASTGRPAVG8',
'FASTGRPAVG16',
'FASTGRPAVG32',
'FASTGRPAVG64',
'FASTR1',
'FASTR100',
'FGS',
'FGS60',
'FGS8370',
'FGS840',
'FGSRAPID',
'FINEGUIDE',
'ID',
'MEDIUM2',
'MEDIUM8',
'NIS',
'NISRAPID',
'NRS',
'NRSIRS2',
'NRSN16R4',
'NRSN32R8',
'NRSN8R2',
'NRSRAPID',
'NRSIRS2RAPID',
'NRSRAPIDD1',
'NRSRAPIDD2',
'NRSRAPIDD6',
'NRSSLOW',
'RAPID',
'SHALLOW2',
'SHALLOW4',
'SLOW',
'SLOWR1',
'TRACK',
'ANY',
'N/A']),
('fits_ke ...
warnings.warn(errmsg, ValidationWarning)
2021-10-05 12:37:19,852 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-10-05 12:37:20,108 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-10-05 12:37:20,110 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-10-05 12:37:20,129 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /grp/crds/cache/references/jwst/jwst_nirspec_refpix_0018.fits
2021-10-05 12:38:25,120 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-10-05 12:38:25,497 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-10-05 12:38:25,499 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:38:25,526 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0025.fits
2021-10-05 12:38:25,661 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2021-10-05 12:38:27,441 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-10-05 12:38:27,727 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-10-05 12:38:27,729 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'dark_output': None}
2021-10-05 12:38:28,203 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0085.fits
2021-10-05 12:38:32,364 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=20, nframes=1, groupgap=0
2021-10-05 12:38:32,365 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=65, nframes=1, groupgap=0
2021-10-05 12:38:34,191 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-10-05 12:38:34,990 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-10-05 12:38:34,992 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}
2021-10-05 12:38:35,128 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-10-05 12:38:35,406 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0020.fits
2021-10-05 12:38:35,704 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits
2021-10-05 12:38:35,751 - stpipe.Detector1Pipeline.jump - INFO - Using 1 core for jump detection
2021-10-05 12:38:36,809 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-10-05 12:38:37,579 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-10-05 12:38:42,770 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 76942 pixels with at least one CR and at least four groups
2021-10-05 12:38:42,771 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 547 pixels with at least one CR and three groups
2021-10-05 12:38:42,772 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 25384 pixels with at least one CR and two groups
2021-10-05 12:38:51,565 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 14.7545 sec
2021-10-05 12:38:51,568 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 16.440006
2021-10-05 12:38:51,572 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-10-05 12:38:52,003 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-10-05 12:38:52,005 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-10-05 12:38:52,574 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits
2021-10-05 12:38:52,626 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0020.fits
2021-10-05 12:38:52,650 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-10-05 12:38:52,651 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/jwst/ramp_fitting/ols_fit.py:1169: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int, :, :, :] *= (segs_4[num_int, :, :, :] > 0)
2021-10-05 12:41:38,595 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 20
2021-10-05 12:41:38,597 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-10-05 12:41:38,877 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-10-05 12:41:39,282 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-10-05 12:41:39,284 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:41:39,340 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2021-10-05 12:41:39,354 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:41:39,527 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-10-05 12:41:39,529 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpsmd6m9t5'}
2021-10-05 12:41:39,592 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2021-10-05 12:41:39,606 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-10-05 12:41:39,607 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-10-05 12:41:39,609 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-10-05 12:41:39,620 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:41:39,881 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-10-05 12:41:39,883 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2021-10-05 12:41:40,084 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-10-05 12:41:40,085 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-10-05 12:41:40,086 - stpipe.AssignWcsStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-10-05 12:41:40,087 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:41:43,717 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_ifu pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0035.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0022.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': '/grp/crds/cache/references/jwst/jwst_nirspec_ifupost_0004.asdf', 'ifufore': '/grp/crds/cache/references/jwst/jwst_nirspec_ifufore_0003.asdf', 'ifuslicer': '/grp/crds/cache/references/jwst/jwst_nirspec_ifuslicer_0003.asdf'}
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-10-05 12:41:51,087 - stpipe.AssignWcsStep - INFO - Update S_REGION to POLYGON ICRS 156.176996289 -45.687617183 156.178772625 -45.687617183 156.178772625 -45.686330364 156.176996289 -45.686330364
2021-10-05 12:41:51,089 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-10-05 12:41:51,096 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-10-05 12:41:51,106 - stpipe.MSAFlagOpenStep - INFO - MSAFlagOpenStep instance created.
2021-10-05 12:41:51,484 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-10-05 12:41:51,486 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-10-05 12:41:51,506 - stpipe.MSAFlagOpenStep - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2021-10-05 12:41:51,508 - stpipe.JwstStep - INFO - JwstStep instance created.
2021-10-05 12:41:51,633 - stpipe.MSAFlagOpenStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-10-05 12:41:51,633 - stpipe.MSAFlagOpenStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-10-05 12:41:51,634 - stpipe.MSAFlagOpenStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-10-05 12:41:51,636 - stpipe.MSAFlagOpenStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:41:51,647 - stpipe.MSAFlagOpenStep - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2021-10-05 12:41:51,775 - stpipe.MSAFlagOpenStep - INFO - There are 5 open slits in quadrant 1
2021-10-05 12:41:51,822 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 2
2021-10-05 12:41:51,854 - stpipe.MSAFlagOpenStep - INFO - There are 9 open slits in quadrant 3
2021-10-05 12:41:51,934 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 4
2021-10-05 12:41:51,964 - stpipe.MSAFlagOpenStep - INFO - There are 0 open slits in quadrant 5
2021-10-05 12:42:07,376 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep done
2021-10-05 12:42:08,100 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:42:08,112 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-10-05 12:42:08,872 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-10-05 12:42:08,875 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.45, 'slit_y_high': 0.45}
2021-10-05 12:42:09,027 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2021-10-05 12:42:09,079 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-10-05 12:42:09,080 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-10-05 12:42:09,081 - stpipe.AssignWcsStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-10-05 12:42:09,082 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:42:09,610 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS2: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
2021-10-05 12:42:09,611 - stpipe.AssignWcsStep - INFO - Computing WCS for 19 open slitlets
2021-10-05 12:42:09,640 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-10-05 12:42:09,641 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-10-05 12:42:09,642 - stpipe.AssignWcsStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-10-05 12:42:09,643 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-10-05 12:42:09,653 - stpipe.AssignWcsStep - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2021-10-05 12:42:09,774 - stpipe.AssignWcsStep - INFO - There are 5 open slits in quadrant 1
2021-10-05 12:42:09,819 - stpipe.AssignWcsStep - INFO - There are 3 open slits in quadrant 2
2021-10-05 12:42:09,848 - stpipe.AssignWcsStep - INFO - There are 9 open slits in quadrant 3
2021-10-05 12:42:09,923 - stpipe.AssignWcsStep - INFO - There are 2 open slits in quadrant 4
2021-10-05 12:42:09,942 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 5
2021-10-05 12:42:10,074 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0035.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0022.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': 'fopens_metafile_msa.fits'}
2021-10-05 12:42:10,654 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-10-05 12:42:10,660 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
Working with slit/slice: 1 bounding box rounded to next integer: [[ 331 2048] [1914 2032]] Max value in slity array (ignoring NANs): 0.4998831147473369 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 2 bounding box rounded to next integer: [[ 46 2048] [1831 1928]] Max value in slity array (ignoring NANs): 0.49994239693485726 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 3 bounding box rounded to next integer: [[ 0 2048] [1638 1710]] Max value in slity array (ignoring NANs): 0.49992568371104673 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 4 bounding box rounded to next integer: [[ 0 2048] [1328 1392]] Max value in slity array (ignoring NANs): 0.49997225701044107 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 5 bounding box rounded to next integer: [[ 0 2048] [1598 1663]] Max value in slity array (ignoring NANs): 0.49996521163224844 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 6 bounding box rounded to next integer: [[ 188 2048] [ 687 766]] Max value in slity array (ignoring NANs): 0.49982756864902916 percentage of F/O trace that was flagged: 99.9
Working with slit/slice: 7 bounding box rounded to next integer: [[ 0 2048] [ 247 292]] Max value in slity array (ignoring NANs): 0.49952809423454014 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 8 bounding box rounded to next integer: [[ 0 2048] [ 171 215]] Max value in slity array (ignoring NANs): 0.4999761295693984 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 9 bounding box rounded to next integer: [[ 0 2048] [1267 1312]] Max value in slity array (ignoring NANs): 0.49986787703942764 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 10 bounding box rounded to next integer: [[ 0 2048] [1237 1282]] Max value in slity array (ignoring NANs): 0.4999627619280446 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 11 bounding box rounded to next integer: [[ 0 2048] [1832 1876]] Max value in slity array (ignoring NANs): 0.49986310206990686 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 12 bounding box rounded to next integer: [[ 0 2048] [1256 1293]] Max value in slity array (ignoring NANs): 0.49992178396516856 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 13 bounding box rounded to next integer: [[ 0 2048] [1695 1731]] Max value in slity array (ignoring NANs): 0.49977105805900096 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 14 bounding box rounded to next integer: [[ 0 2048] [1635 1667]] Max value in slity array (ignoring NANs): 0.4999166217521449 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 15 bounding box rounded to next integer: [[ 0 1980] [1379 1407]] Max value in slity array (ignoring NANs): 0.4999679347315006 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 16 bounding box rounded to next integer: [[ 0 2033] [1863 1895]] Max value in slity array (ignoring NANs): 0.49992408655614395 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 17 bounding box rounded to next integer: [[ 0 1989] [1519 1548]] Max value in slity array (ignoring NANs): 0.4998243708705976 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 18 bounding box rounded to next integer: [[ 0 1838] [ 208 229]] Max value in slity array (ignoring NANs): 0.4999277036218135 percentage of F/O trace that was flagged: 100.0
Working with slit/slice: 19 bounding box rounded to next integer: [[ 0 1828] [ 626 649]] Max value in slity array (ignoring NANs): 0.4999228119213873 percentage of F/O trace that was flagged: 100.0
*** Final result for msa_flagging test will be reported as PASSED ***
('* MSA flagging validation test took ', '24.889929056167603 seconds to finish.')
Did msa_flagging validation test pass? True
# Quickly see if the test passed: Do the NIRSpec implementation and the pipeline's agree within <= 99.5%?
print('These are the final results of the tests: ')
for key, val in results_dict.items():
if not isinstance(val, str):
if val:
val = 'PASSED'
else:
val = 'FAILED'
print('{:<40} {:<8}'.format(key, val))
These are the final results of the tests: mos_prism_nrs1_uncal.fits FAILED mos_prism_nrs2_uncal.fits skipped mos_g140m_line1_NRS1_uncal.fits PASSED mos_g140m_line1_NRS2_uncal.fits PASSED ifu_prism_nrs1_uncal.fits PASSED ifu_prism_nrs2_uncal.fits skipped ifu_g395h_f290lp_nrs1_uncal.fits PASSED ifu_g395h_f290lp_nrs2_uncal.fits PASSED